Compare the specs of a file converted with v1 that works in your player to one that you've prepared with v3 that you think should work, but doesn't. The following utility will help:
http://mediainfo.sourceforge.net/en
Adjust your conversion parameters accordingly with v3.
If this doesn't work you can also try opening up convert.ini file from V3 and editing the conversion parameters directly to match those of v1 or replace the coding command lines only with those that work from v1 and see if this helps.