Auto Tagging Deletes Terms From All Tag Volcabularies Even if They Are Disabled

If I create 3 vocabularies with the following settings:

(Vocab 1) - Required, Multiple select, Disable autotagging
(Vocab 2) - Multiple select, Disable autotagging
(Vocab 3) - Multiple select, Autotagging enabled

then the auto tagging works great and does what it is supposed to. Additionally, all vocabularies are shown. Now if I change vocabulary 2 to the following:

(Vocab 2) - Tags, Multiple select, Disable autotagging

then if I save a node with terms in vocabs 1 and 2 selected, then the terms from vocab 2 do not show but vocabs 1 and 3 show terms. If I edit the node, the terms I selected for vocab 2 are not there. I try again and the same result occurs: the terms are deleted. If I change the settings of vocab 2 to uncheck the tags setting, reselect the terms of vocab 2, then they show up for vocab 2 now when the node is saved.

Has anyone else encountered this? I tested version 1.25 on a fresh D6.13 install with only the modules necessary for auto tagging.