The FoolishIT protection tool installs a set of commands that disallow any encryption of your files. Not sure what sort of workaround you could come up with the get around that.
It's also possible to do it manually. See here:
Looks like some sort of change in the registry under policy settings. It would be fairly trivial for the virus writer to change the policy back before doing their dirty deed. Whether that makes sense for them depends on how many people use this form of “protection”. Remember Windows is “protected” to begin with but that doesn’t stop virus writers or even slow them down much.