Hello Mr. E,
I am also having the same Issue "Transaction Id already queued for package ###".

I am using BES 4.1.3.
And I tried to run the query suggested by you.
UPDATE ITAdminqueue SET GroupingNumber=0 WHERE command=3
-- Result -- No row affected
DELETE FROM ITAdminQueue WHERE GroupingNumber <> 0
-- Result -- Some number of rows affected

Again, after some time when BES poll for Missing Apps. POLC log again shows
"Transaction Id already queued for package ###"

Any idea what may be going wrong here?

Thanks and appreciate your reply,
Hemant