I believe that this error has something to do with a mismatch between my tiedlist and the hmmdefs (as pointed out here:http://www.ling.ohio-state.edu/~bromberg/htk_problems.html), but I can not seem to solve it. All of the triphones in my corpus are present in my triphones1 list and triphones1 only contains monophones,biphones and triphones from my corpus.
If I take said triphone out of the triphones1 list and recreate the tiedlist it passes but complains about another triphone down the road. Obviously manually taking out all of these triphones would take me years and it doesn't seem efficient which leads me to believe that I have missed something further back.
It is also important to note that all these triphones generating errors are in my corpus as well. To me this error would only make sense if I had unseen triphones somewhere, but where? I feel that I have left no stone unturned but surely someone can give me a fresh idea of where to look.
There was an extra AU command at the end of the tree.hed file This was causing it to try and open another file after the tiedlist. I am not sure why this causes an issue when it has already accessed tiedlist, but there you go.
Hopefully this serves as a extra check for future htk users.