So you're using Synergy to use your Mac and Windows machines as one; you press Ctrl+C on Windows to copy, move over to a window on your Mac OS X machine, press Ctrl+V to paste, and it doesn't paste what you just copied, right?
If your problem is the same as mine was then I can help you: if you're using a Windows keyboard with Synergy, note that on your Mac OS X computer you'll have to press Windows+C and Windows+V. That is because by default the Windows key maps to the "Open Apple" key on Mac keyboards, and the copy/paste shortcuts on Mac is Open-Apple+C and Open-Apple+V.
It'd be nice to be able to just switch the functions of the Ctrl and Open Apple keys while on the OS X client -- and I just put in a feature request to Synergy for key mapping. OS X allows you to swap modifier keys like that; the problem is that if Windows is your Synergy server and OS X a client then the keyboard input OS X receives is not from its own keyboard but rather from over the network and therefore you can't configure it (I tried it). So until Synergy has such a feature, you'll have to learn a new skill of swap-erama.
If that's not your problem, then I'm sorry, I don't know how to help you (Especially considering I don't even know that you're reading my article right now, let alone what your specific problem is...).