I'm going to try and figure out whats going on with both of these issues. The virtual control code for the 396XT is that exact same as is used for the 346XT, and thats what I use to test with. It seems to work on my end, which makes me wonder if there is some option set on the system or channel that is changing the way it gets logged.
Going to look into the alert colour. You say "upload from the scanner", do you mean download?
Glad to see that FTO is working right though, seems like that was always a troubled area.
I'm using a BCD396XT and have also noticed that 0.9 does not log conventional channels. It seems to log trunked channels OK. Note that if the scanner is stopped on a conventional channel (i.e.: the squelch is open) and I hit the hold button in virtual control mode, the logger does log the conventional channel hit.
Also, I have noticed that the alert colours are not uploaded from the scanner for conventional channels. The alert colours/tones are uploaded for trunked channels and in the fire tone out settings, but not for any of the conventional systems.
Regardless of this, thank you for a great program!