As was mentioned, the packaging difference is due to one being exclusive to Wal-Mart while the other goes to everybody else. That said, there may be something to the whole "two factories/lines" thing.
Pretty much only ever buy Federals - usually from Wal-Mart (about the only reason I'll go into the store). Like the bullet a lot, but supply started getting scarce and I hated stopping at the store to leave empty-handed. Decided to try ordering online from Cabela's during a sale. Got the Federals (525 packs instead of the 550s) and Wow, there was a difference. Generally, the bullets I got from Wal-Mart looked shiny, polished, and nice. They fed like a champ through all of my firearms. The stuff I got from Cabela's, however, was dirty and nasty-looking, like they were coated in wax somebody had chewed on. Gives my 10/22 fits trying to chamber it although it seems to shoot fine. 3 of the 4 boxes I got were like this - haven't opened the last yet, but I imagine it's the same.
I seem to remember hearing not too long ago that Federal was bought up by CCI or vice-versa. Perhaps that has something to do with it.