Windows DVD maker that comes with Vista probably has an encoder not as good as TMPGenc
Encoders are far from equal in abiltiy
I dont think WMM is the "weakest link" here
In absolute terms as well as quality of encoder, you will need to specify the encoding bitrate , and whether you want to do a Constant or variable bitrate, 1 or 2 passes
All these affect outcome and it may be that TMPGenc default setting are better than the Windows versions, Im not familiar with it enough to know how customisable its setting are
HTH
Otherwise you may need to try something not WMM and DVD maker .....