That's a problem with the aspect ratio flag in tmpgenc.
Unfortunately I haven't been using it for a long while.
There should be an option in tmpgenc named "target aspect ratio".
Please set that as "center".
And please use an avisynth script as an input in tmpgenc if you're not doing so already.
If you don't know how to setup a script then use Incredible's PARanoia.
It even has it's how sub-forum here at kvcd.net.
Do install XviD to take care of YV12 colorspace input and tmpgenc's ReadAVS VFAPI plugin so that tmpgenc can load avisynth scripts.
You can find all the info on the forum using the search engine but you can ask for help if you run into any problem trying to set it all up

.
Cheers