If you are using HTK still and has headaches with it, you have last chance to move to CMUSphinx! You can even take your models with you!
The htk2s3conv package which converts HTK model to SphinxTrain format has been landed in our VCS recently, check it out at
https://cmusphinx.svn.sourceforge.net/svnroot/cmusphinx/trunk/htk2s3conv
Don't forget to read the documentation!