My first idea to your problem ... make sure, that no other application have access to the files, while Mp3tag writes to the files.
RESPONSE: Mp3tag is the only open application used at the time when tagging these files, no other files, applications or processes are collecting information on these files.
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My second idea ... which track related tag-fields are stored within the mediafiles, ...
and do they contain the correct values, for example: TRACK and TOTALTRACKS ?
RESPONSE: When writing metadata for these files, all fields are ALWAYS blank to begin with - I tag freshly and cleanly from beginning to end. ~PERFECTIONIST~