First note : 128 minute fullscreen must be done at 352*288
(perhaps 352*576 but few movie are correct with that).
For CQMatic :
1/ your first problem is proabaly due to the fact you didn't reset the source range editing before to uncheck "source range". That means that you must go in the source range window, clic on "default", then clock in the menu at the left and select "reset cut editing". then exit form the window AND uncheck the source range check box.
You need to do that anytime ! Just unecheck the box is not enought.
2/ your secodn problem : be sure to have the "audio source" empty in tmpgenc. CQMatic does not work if you have something there.
(idea : before to restart cqmatic, go in the directory where the exe is and remove the 2 cqmatic*.tpr files that are there- they are somtimes corrupted and makes things going crazy).