I bet on setting in your player, if you're absolutely sure that the VOBs and their sources were correctly flagged (16:9 respectively 4:3). You can check this, at least I do, with DVD patcher.
These settings should match the type of TV you have. Check the manual how to do this.
However, if you mixed 16:9 with 4:3 within the same track (you can fool TMPGENC, because it checks only the first header not the actual content) now you have problems.
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