The original problem for the duplicate ID was MobileMe. That was acknowledged by Apple to me at the time, however they could not completely correct the issue at the time by merging the accounts (and still can't). Fine. They were able to get it where I could use all the albums I had purchased up to that point even if they were not merged. That was good enough for me and I have been happily using everything for the last 5 years using only one of the apple ID's. The incomplete fix, that being the old ID that was really still there lurking in the background with some of the albums still attached to it, only resurface when the combination of the two issues happened:
1) the iTunes Match / iCloud / cloud / [whatever you want to call it] corrupted the entry whereupon I could not download it to play on any of several devices.
2) seeing that it somehow got corrupted, I thought fine, I will do what others had done on the forum and simply delete it, then re-download (since I had already purchased).
The album was not detected as being already purchased (due to the old ID I had long forgot about), and I was charged again.
If I was alone in these issues I would say "Dumb me, this setup works perfect and I need to read the directions better". If you search around you will see zillions of other people with these issues and more.
As far as my confusion with the iTunes and iCloud you will find the following on Apples website (including this from a simple Google search):
www.apple.com/icloud/features/Share
iCloud stores your music, pushes new purchases to your devices, and lets you download past purchases from whichever device you're using.
Hmmm. I don't know where in the heck I would I get the impression there was any connection.