My skin has been fine, absolutely perfect since about month or so on doxy bar these very minor breakouts ever couple of weeks. I have noticed if i do get a spot though, its not as inflamed/red as before and it go's really quickly, which is good. I just hope, being in my 9th week and all, the minor breakouts stop as well, as yours have.
Regards your concerns, I guess its just the same everything else... works for some, doesn't for others. All you can do is hope. Without hope we'd all be screwed. Tetracyclines have been known to cure the most severe of acne in some cases, i guess its just luck!
Don't worry. Enjoy your clear skin!