Turns out not user error:
I have attached two MP4 files tagged with metadata to outline a potential bug in MP3Tag v2.45a.
The first "1_stik_tagged_by_MetaX_is_9.mp4" is a file tagged by MetaX. In this file, the contents of the "stik" tag used by iTune to identify whether an item is movie or tv show, etc.
In this file, you will see that the stik tag has a value of 9.
I then open this file in MP3Tag, and immediatly apply an Action, containing the items shown in the attached JPG. Once the rules are completed, the stik tag's value has been unwantingly changed from 9 to 0 (as seen in the file named "2_stik_tag_after_actions_in_mp3tag_is_0.mp4")
I noticed that this does NOT occur when you simply open the original file, and immediatly press save.