Oddly enugh running the command line to convert books that previously froze the program (both html and lit) works flawlessly. The resulting book can then be imported into calibre and passed on to the reader. The issue is only when the conversion is run from the gui.
I've verified I only have the single copy of any2lrf on my system as well if it helps.
This will around to allow me to continue using the MCE system for my library