Control+V has never worked for me in the command prompt, that has nothing to do with StrokeIt. However, I have just found 7Plus, which has many features, one of which is just that, making Control+V paste in command prompt. I have just tested it on XP, and it works.
In order to combine it with StrokeIt, I had to make a special action for the application Command Prompt, because it wouldn't work with my normal Paste action, which has an OSD + sound.
http://code.google.com/p/7plus/wiki/Features#Misc
StrokeIt is fantastic! And it has great synergy with the (freeware) program Autohotkey; just make a gesture to produce a hotkey that will trigger a function in AHK: you can thus get a gesture to do anything.