So I checked out the old version of mapconv from svn to try and and see where the trouble was. It turns out that mapconv uses an outdated set of parameters for nvdxt, that were hard coded. Unfortunately I was not able to recompile it from the svn source, as several files were missing and it required some funky old boost lib I counldnt get

So I tried the next closest thing; I wrote a tiny program that masquerades as nvdxt, and forwards the call to it from mapconv, with setable parameters.
My bit of code is named nvdxt.exe, and I renamed the real nvdxt.exe to nvdxt2.exe. This way, i can forward this call: nvdxt2.exe -file temp\*.bmp -nmips 5 -dxt1 -box -fadeamount 0 . Which results in a complete lack of scanlines. Beware, this is the default line and is set to high quailty, so it will be slower than previous compilings.
Also included is the latest version of nvdia's nvdxt.
Usage:
Download it here from jobjol:
http://spring.jobjol.nl/show_file.php?id=1745
To install, unzip the contents to the dir where you use mapconv.
Then just run your compilation .bat file as normal.
To change nvdxt options, create an nvargs.txt file next to nvdxt, and add the line you want it to use for compiling.