Sure, it's probably something wrong with the charging circuit. My guess is, the battery died because it wasn't being charged. The fresh battery doesn't have enough juice to perfectly run the bike, so it's running in "limp home mode" which is why it makes noises and has a low max RPM. Just a guess, but it's one that fits the given facts.
Call the dealer and ask if they've checked that… should be an interesting response! LOL
Call the dealer and ask if they've checked that… should be an interesting response! LOL