What is the actual version of each instance where this occurs? It could be a bug in the maintenance plan task - where it only performs the backup task on the master database.
I saw something similar to this in 2005 - but that was on the integrity check task and that one would loop through each database and perform the integrity check on the master database for each database in the collection.
It could also be a misconfiguration of the backup task, have you tried recreated the backup task and making sure you have reselected all databases?
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Managing Transaction Logs