I second your problem. Ditto for me on the Purchases.
I'm in the middle of an email exchange with iTunes support. About 5 exchanges so far with responses that clearly show me, the person at the other end is using some form of pre-written template answers and not reading my email or understanding the problem.
In the end, they just initialize your purchase history to re-download all your songs, with the warning that this is a "one time" event.
*** ? What's the point of the new "Purchases" feature then ?
In addition to your problem getting mixed m4p & m4a files for the same song from old purchases, my "refresh" of my entire purchase history just caused a very recent (2 week old) purchase that was never upgraded but bought in iTunes Plus 256kbps format to revert to the older DRM protected 128kbps!!
Clearly there's something mixed up in the way they're handling their metadata ids and customer references.
I've sent a slightly stronger worded (but not rude) email to their support asking for some form of escalation.
It's one thing for years old files that I originally bought in m4p format not to have ever been offered for upgrade to be redownloaded the same way, but another thing entirely for recent DRM-free purchases to be reverted to the DRM protected format and then have the existing good files trashed.
Good thing I have backup copies, but it's quite annoying to have to spent hours on searching for mistakes and fixing currently 800+ purchased song files.