The foundation fee is not specific to potcoin, it has always been the developers intent to implement that function with particular licensed partners of the wallet program.  In such an activation event the "Foundation", who is a registered non-profit, gets a licensing fee to maintain the software.  That is why the code exists.  It is not nefarious but an intended feature of the wallet program.  It's a holdover from the original bitcoin wallet.

And NO on the windows version, the potcoin wallet devs don't do winblows.  That windows version was compiled by another party.  

For what it's worth it should be easy to test if some percent is disappearing from the wallet and someone would have noticed a 2% fee long ago.  (Though few would notice a few missing satoshi).