Appears to be ISBoxer. I switched to Keyclone to launch windows. FRAPS will still lose focus eventually, but I can safely close it and reopen without them shitting out.

Whelp that sucks, no more video fx.

*Since this is definitely an IS issue, I respectfully request a complete refund for my licenses + additional fees for the mental stress this has caused. I anxiously await a response from Lax regarding my request. Thanks.

*sarcasm