Ok, lets start with a small post….a BizTalk 2010 update is released (CU4). The approach might be to install it when you have issues, although there seems to some minor changes on EDI handling, please note the following trivial changes;
2672494 (http://support.microsoft.com/kb/2672494/ )
FIX: The BizTalk Server MessageBox database grows very large because records are not cleared in the EqualsPredicate2ndPass table in BizTalk Server 2010
2662532 (http://support.microsoft.com/kb/2662532/ )
FIX: A "Backup BizTalk Server (BizTalkMgmtDb)" job on BizTalk Server 2010 fails when you try to back up a custom database.
Although the update might be not suited for you due to company policy of only installing Service Packs,you should at least check out if the MessageBox database is indeed very large and all jobs are running smoothly!