Yep, PunkBuster and Steam Overlay do not like each other. It's PB that is the problem, this has been happening for over 5 years now. For WAW you have two options:
1. Disable the Steam Overlay, you don't have the Steam overlay when playing WAW but you can play on PB servers.
2. Only play on non PN servers, you may face a problem here as there are not many servers left on WAW currently never mind non PB ones.
I think option 1 is your best bet.