I'm using Atmel Studio 6.2, Arduino 1.6.4, Visual Micro 1505.19 sp4.  The boards that show up in my list are the ones that were already set up in my Arduino IDE when I first set up VM: Arduino core, and Adafruit (added with Arduino IDE's Boards Manager).  I have since added some Boards Manager urls in VM's IDE configuration screen (and also added them to Arduino's url list, in the course of troubleshooting this problem.  didn't help).  These urls successfully load their contents into the Manage Boards tab of VM Explorer.  When I click a new board type, and install it, it appears to work in VM (the board greys out and become listed in the Installed section).  And it does work at some level (if I go to the Arduino IDE, it does have the new boards installed).  But the boards never actually become available to VM to use (not in the shortcut bar, Tools menu, etc.).  And if I close VM Explorer and open it again, the boards that I just downloaded are back to their uninstalled status, not greyed out and no longer in the Installed list.  VM will then happily "install" them all over again.

Clicking the "View user hardware folder" link at the bottom of VM Explorer gives the error "The system cannot find the file specified".  Not sure if that's related, but VM seems to have found the rest of the bits of my Arduino IDE (including the extra boards I had added before installing VM), so I'm not sure why it's balking now.  This is a pretty fresh install of windows on this computer, and I'm pretty sure I don't have a manually added hardware folder anywhere.  I've only used the Boards Manager on this computer.

I have uninstalled and reinstalled VM several times now, with reboots and everything, and this issue persists.  I noticed that the shortcut bars never really go away, even after uninstalling, they just become empty.  The Tools>Visual Micro menu does disappear, though.  At any rate, after every reinstall of VM, every attempt to install with the board manager, etc., the boards list only ever has the things it discovered when I initially installed VM.

Yeah, I would expect to only have to add the urls in one place.  I had tried adding them to Arduino IDE's list early on, because I had noticed that the only ones that actually worked were the ones added through the Arduino IDE.  But adding them to Arduino IDE's list after the fact did not help.  My list of boards is still frozen at what it was when I first installed VM.

1: I have done both those things, numerous times throughout the process.   
2: Arduino 1.6
3: I just looked, and I can't actually find anywhere where it says what version I have installed.  I downloaded the version from the "Download Latest Visual Micro" link on the main download page just yesterday while going through the uninstall/reinstall cycle.  Underneath the download link it says "(version 1505.19 Sp4 released 30th May 2015)", so I'm assuming that's the version I've got.  Any way to verify this?  And if that is truly Sp4 and not just an unupdated description on the download page, where do I find Sp6?

OK, I set the contributions path to a test folder.  It was blank initially.  Should it have already been set to something?  Anywho, after setting that folder, under Manage Boards in VM Explorer, only the base Arduino boards showed as installed (not my Adafruit ones).  When I clicked the Adafruit ones to install, it finished in virtually no time.  When I clicked the other ones I have been trying to install, it took the minute or two it usually does to retrieve and install the files.  After clicking Rescan, the two new ones, that actually took time to download and install, disappeared.  But the Adafruit ones remained installed and available.  E-mailing you the results of the trace now.

Edit: The newly created contributions folder does appear to have the files for all three (Adafruit and the two that don't load).  The other two are for the bare atmega and the attiny, from the webpage linked from the VM configuration, with safe urls.

Edit edit: Tried with the ESP8266 url too, to see if maybe it was something particular to the two I had been trying.  Still no dice.  Appears to install, and files end up where they should in the contrib folder, but on a Rescan it goes back to appearing uninstalled, and never becomes available in the boards drop-down.

The following are the jsons I have added in VM configuration:

https://adafruit.github.io/arduino-board-index/package_adafruit_index.json

https://raw.githubusercontent.com/damellis/attiny/ide-1.6.x-boards-manager/packa...

https://raw.githubusercontent.com/carlosefr/atmega/master/package_carlosefr_atme...

VM Explorer is also showing me the contents of the following json's that I entered into the Arduino IDE's url list but not VM's:

http://arduino.esp8266.com/package_esp8266com_index.json

https://dl.dropboxusercontent.com/u/2807353/femtoCore/package_femtocow_attiny_in...

From all those, I have been attempting to install the attiny 1.0.1, the barebones atmega 1.1.0, and most recently the esp2866 1.6.4-673-g8cd3697 (but only to see if it would work, I don't intend to use it).
So far, nothing has installed.  The only boards VM sees are the ones I had added before initially installing VM.  Even adding the boards through the Arduino IDE, VM doesn't recognize anything other than the core and Adafruit ones.

Edit: not sure why it's splitting some of those urls into two lines.  It shows up as one line when I am editing the post, but gets split when I save.

Edit edit: This morning I tried uninstalling everything.  VM, Atmel Studio, Arduino, all of it, and reinstalling.  But the uninstalls don't do a very complete job, apparently.  After reinstalling, and before doing anything about boards manager, json url's, etc., everything is back to how it was.  Core + Adafruit installed, all the same board manager url's configured, etc.  Still can't install any new ones.

Edit edit edit: It was still looking at that manually configured contrib folder I created earlier (another setting that survived a complete reinstall).  When I cleared that setting and let it go to the default folder, it had only the core files (Adafruit not installed).  And upon trying to install the barebones atmega boards...  it worked!  Go figure.  I have absolutely no idea what was stopping it from working before, or what made it work now, but...  it does, so hurray?

Edit edit edit edit:  Argh!  After seeing the attiny and barebones boards install and work, I installed the Adafruit ones, too.  As soon as I installed them, it wiped out the attiny and barebones boards.  I was unable to reinstall them, even after uninstalling the Adafruit boards.  So now I'm right back where I was.  I can install the Adafruit boards and have them stick, but everything else disappears on a Rescan.

Edit 5: If I delete the entire Arduino15 folder in AppData\Roaming, then I can install the attiny and barebones boards.  I guess for now, I'll just avoid installing the Adafruit ones.  This whole thing is so bizarre...

Well, I'm assuming it's got something to do with some setting or configuration that lurked on my computer even after uninstalling all the relevant programs (Atmel Studio, Visual Micro, Arduino IDE).  If it was the Adafruit url itself, loads of people should have had this problem.  So I've gone scorched earth and wiped the entire laptop to start over clean.  I'll let you know how that goes once I get through the interminable windows update cycle and can get software reloaded.

Yep, it certainly seems to stem from using the Adafruit url.  I tried including it last in the list of urls to see if the other stuff could load before it throws a monkey wrench in, but no dice.  But if I keep it out of the picture entirely, everything else works fine.  And the core boards include the Gemma, which means I can still program my Trinkets.  I guess I'll just leave it at that for now.

Thanks for the update.

Visual micro uses the SharpZipLib library to unzip the tar balls, bzip, gzip files etc of each core. It's been a problem with the esp8266 hardware, I had to tweak the SharpLibZip library source to "sort of" get it working.

So we will move over to using 7Zip or something that might be more reliable in future releases of visual micro. Sad because for normal zips and most artchives from most sources the SharpZipLib has proved to work well