For people who're affected by this "communication error", or have done modification of their Platinum/HG/SS save files with Wonder Cards, manual modification of the save file will be necessary to remove the data improperly set by PokeGen. (This should not be done to Diamond/Pearl save files, and this problem does not affect Black/White or Black 2/White 2.)
Bytes from 0xA7D0 through 0xA810 and 0x4A7D0 through 0x4A810 (NOT including the byte at 0xA810 and 0x4A810.) should be set to 0. (Well, I can't say with certainty that they should be 0, but every file I've seen so far has zeroes. Zeroing it out does fix the problem, however.) You can do this directly to your save file, load it with PokeGen (Which will tell you it can't identify the save game, at which point you force it to load as the appropriate game.), then save. That will recalculate the checksums to make the file work again.