I'm guessing that PainKiller is SD 3.20.022, just like Far Cry and Splinter Cell Pandora Tomorrow. This protection has blacklisted CloneCD's Hide CD-R media.
I have CCD installed and run both Far Cry and Splinter Cell Pandora Tomorrow but without the CCD Tray.
The only other thought I have is that there are some registry entries left over from when the CloneDrive was installed that the protection is picking up on. Just don't ask me what they are - because I don't know. Last time I built my machine I deliberately didn't install the CVD.