In my experience, whenever I attach media to citations that were made by Ancestry.com, that media is never uploaded to my AMT. The workaround I use is that I upload the media item to my AMT, sync it back to FTM, then link the media item to my citation media. Another alternative probably is to just link the media item to a person (independent of the citation). I think the uploads are only suppressed when they're only linked to citations from Ancestry.com. Try it.
As for people not synchronizing, that is surprising. I have encountered numerous instances where my tree has become out of sync. Generally that involves facts, citations, and media. I've never seen it with people.
From a programming perspective, one solution to this problem is to create an option for a full sync. I think the way that it works now is that it only looks at items that meet certain date criteria, so that once something slips past the sync code, you shouldn't expect it to be found in a subsequent sync, because the dates associated with its data aren't included in the data considered for synchronizing. That's where this full sync comes in. The idea is that each database is fully compared to the other. It's something that could be used in special situations to fix problems. It wouldn't, however be the default synch'ing mechanism, because it would be too inefficient. This isn't a novel concept by me, and I'm sure it's something that the product development team has discussed. I'm just not sure if it's possible to get them to fix it by this or other means.