Sorry guys but the secret of this bad resizing problem is within TmpgEnc
If you FIRST choose the template and THEN the sourceinput .... by this the size encoding settings will switch to the resolution which COMES with the source as input.
So FIRST do import the source and THEN choose the template and your resizing to 352x288(240) or whatever should end up right.
So do your test as recommended by dialhot and you will see that your re-encoding still got the resolution as it was given bei the SOURCE.
(I hope i didn't read to fast again the last replies, but to me it seems that this could be the problem of D-Mouse