I don't know man, I have never heard of purchases being transferred to another account, and, if this did happen with you, you are unique. And as far as iTunes databases, I've been using iTunes since it's debut in 2001 (wasn't it 2001?) and they have been transferred between three Macs. There are even times when I have just dragged databases over. Maybe it's because I know what I'm doing, I don't know. I'm not saying that to cut you down, but it always amazes me how some people have nothing but issues and problems and for others, it all works fine.
Regarding the transfers: I had a good selection of music and a few apps. If they were still linked to my 'old account' they wouldn't play, and yet they do. The get info for the tracks shows they were purchased prior to when the schism happened. I don't know how, but it happened.
iTunes database: Well, I admittedly do things that probably ask for it...
I *HATE* the way CDDB sometimes gives up creepy metadata for CD's I rip. I ripped a 4-disc set once, and the info from CDDB had no consistency at all from one disc to the next! I was ticked because I knew that I'd have to go back and fix it... The way the CDDB database is organized is just ridiculous, although it does save time from having to enter all of the track data manually. I bought and extended edition CD once, and noticed that when I was ripping it, it didn't have track names for the last few bonus tracks. I thought 'Really? Isn't that special.'
Obviously iTunes is reading some code or such from each disc, and then runs out to CDDB to get the metadata, but who creates the metadata in the first place? (I had a CD rip with Chinese encoded track names once. That was special)
But I go in and from time to time 'cleanup' my iTunes database, shuffling names, combining multi-disc sets so they show up better in iTunes. Correcting misspellings, removing the redundant (LIVE) notations on a ripped CD of a live album. (Um, hello, it's a live album. All the tracks are 'live', do you really need that to remind you?)
And usually when I've had issues it's during a prolonged session of fluffing the track info.
The last big rant I went on with iTunes was to get the pod casts to not show up in the 'Music' listings. Don't know if that's common or not.
But here I am ranting again about iTunes and flaky metadata... I could probably go on all day.
But, yeah, I've probably done a lot of that to myself. (I even, once, had to hack the iTunes database directly to fix a problem. That was years ago though. Many rebuilds ago...

)
But anyway...