If I do that without loading the jungo drivers, In the Serial Port window beside Arduino 1.5x Uno the port is set to 4 but according to device manager the port is actually 5 and I cant see how to change it. 
At the end o build I get:
Uploading to I/O board using 'COM4'
Flushing the serial port
The port 'COM4' does not exist.
I will experiment with the jungo drivers later, I have to go out now.

OK, still using the Arduino drivers, Device manager says, Ports (com & lpt) - Arduino Uno (com 5)
Re-powered my PC and the Arduino environment reports UNO on com5 and I can upload to it.
Going to V Studio and V Micro (sorry I confused the V etc) it still reports on com4.
In V Studio - Tools - V Micro - the other serial poers is disabled so I cant change to com5.

Just going to get information for your other questions.

1) I guess you have a "sketchbook folder\libraries folder" with a few custom libraries installed?

C:\Users\Jim\Documents\Arduino\libraries is empty
C:\Users\Jim\Documents\Arduino\hardware had  a Tiny folder containing the cores for ATtiny devices.
I removed the Tiny folder because it relates to arduino 1.0.5 anyway. This made no difference.

2) Do you see any libraries listed on project>add/import sketch library>user?
I see: User which is disabled blanked.
         Core which has a list starting with EEPROM

As concerns uploading I still need answers to these two questions please

Can you see the Uno listed under tools>visual micro>serial monitor? Is it ticked?

1) Did you un-check tools>visual micro>upload using programmer"?

Yes

2) If you untick "upload using programmer" in Visual Micro and also select the serial port from "tools>visual micro>serial monitor" then press F5 what happens?

Serial monitor is still trying to use com4 instead of com5

Windows 7 home premium.

I am still not using the jungo drivers, should I try them?

Please also switch off "tools>options>vm>communications>network discovery" this will give you the old style ports list.

If the port list is wrong then I will give you a link to a simple c# app that shows what windows things is the current port list.

Thanks

Great. Okay I want to explain some things about what has been happening but first I want to be clear about some thing which you might already have realised. 

Quote:


1) The COM problems you encountered were due to the fact that your windows 7 wmi database is slightly corrupted. I have read on the web that this sometimes happens and there are, for windows 7, some simply fixes. I haven't tried any fixes because I do not have the problem. 

You can see the type of code that Visual Micro uses to get serial port names using this microsoft tool: http://www.microsoft.com/en-us/download/details.aspx?id=8572

For example I just used the tool to produce this

strComputer = "."
Set objWMIService = GetObject("winmgmts:\\" & strComputer & "\root\CIMV2")
Set colItems = objWMIService.ExecQuery( _
    "SELECT * FROM Win32_SerialPort",,48)
For Each objItem in colItems
    Wscript.Echo "-----------------------------------"
    Wscript.Echo "Win32_SerialPort instance"
    Wscript.Echo "-----------------------------------"
    Wscript.Echo "Description: " & objItem.Description
Next 

Actually Visual Micro uses a C# equivalent with the  ManagementObjectSearcher

2) To fix the wmi on windows7 I have found this untested suggestion on the web

winmgmt /standalonehost
winmgmt /resetrepository 

3) Libusb-win32 should work in Visual Micro if you have ticked the standard AVRISP mkII

4) Jungo should work in Visual Micro if you have ticked Atmel AVRISP mkII

5) In both cases 3) and 4) with tools>options>visual micro>compiler>verbose you will see the command line that Visual Micro us running to invoke the tools that control the programmers. So you will see that Visual Micro does not know the usb driver it just runs the appropriate tool.exe for the selected programmer. 

I think this means that you have some other issues on your pc. An easy test, with Jungo install, is to see if you can use the standard atmel studio tools>device programming dialog to upload your .elf. I expect you should see the same error that Visual Micro encounters. If not then we I can ask Atmel about it but please open a new thread purely for Jungo/Atmel programmers

Again to solve the win32 libusb error also please open a new thread because it is standard stuff and is generally working okay

Both of these last issues might still be related to a corrupted wmi database but that is a wild guess.

I hope this helps

No problem. Other users will just think that Visual Micro doesn't work so it was very useful that you also invested this time in helping to understand the cause of this issue.

We have already altered the new help system (due shortly) to include some helpful tips as a result of your post and will continue to consider how we can auto-detect and warn users if this happens. It's a difficult one and I need to go back through the forum logs because I suspect someone else has encountered the issue but I didn't have the detailed answers to determine the cause!

So thanks