So I got your files and compiled and received the same error. By turning on verbosity with -v:2, I can see the csc.exe invocation:
C:\WINDOWS\Microsoft.NET\Framework\v3.5\csc.exe "/r:Cobra.Lang.dll" "/r:C:\WINDOWS\assembly\GAC_MSIL\System.Windows.Forms\2.0.0.0__b77a5c561934e089\System.Windows.Forms.dll" "/out:x-uno-win-form.exe" /nologo /nowarn:0108,0162,0169,0183,0184,0219,0414,0429,1717,1718 /main:MainWrapper /win32manifest:addUAC.xml -lib:"C:\Documents and Settings\Chuck\My Documents\Projects\Cobra\Workspace-B\Source" "x-uno-win-form.cobra.cs" "MainWrapper.cobra.cs"
I then cut it down my making the /r: to WinForms use its simple name rather than the full path:
C:\WINDOWS\Microsoft.NET\Framework\v3.5\csc.exe "/r:Cobra.Lang.dll"
"/r:System.Windows.Forms.dll" "/out:x-uno-win-form.exe" /nologo /nowarn:0108,0162,0169,0183,0184,0219,0414,0429,1717,1718 /main:MainWrapper /win32manifest:addUAC.xml -lib:"C:\Documents and Settings\Chuck\My Documents\Projects\Cobra\Workspace-B\Source" "x-uno-win-form.cobra.cs" "MainWrapper.cobra.cs"
And that compiled with no errors. Then I tried with:
@args native-compiler:"C:\WINDOWS\Microsoft.NET\Framework\v2.0.50727\csc.exe"
And had the same problem with the same fix.
So at least we know this is not caused by .NET 3.5 nor by /win32manifest. I don't have a workaround (given that you want to invoke the csc.exe of .NET 3.5). I have major client work Monday, but will try to get a fix in with a test case to lock it down, as soon as possible. Or patches are welcome.