I'd have a look what transactions and which databases the version store is generated for. It might give me clue regarding what process may be responsible for the issue.
But I never came across this issue myself, so it's pure speculation at this point.
It looks like sys.dm_tran_active_snapshot_database_transactions might contain the information you are looking for.
Regards
Piotr
...and your only reply is slàinte mhath