Hi,
Same problem. channels 4 and 5 set to gtr sounds just ceased to work for me, but as you say Halion registering the midi in, but not outputting any sound. I was running quite a few instruments and thought it might be a polyphony issue, so I reduced polyphony on all instruments to no avail. I set up the sounds again on channels 11 and 12, they worked for a short time and then went dead. Have you had any luck resolving this since you posted the issue.
Cheers
Geraint