Hi Craig,
I can't really explain your AF problems but it would seem to me that it's better to trust the Bahtinov mask (despite what the numbers might suggest). I don't know the ASIair device but there are a couple of things to consider for autofocus routines. When using NB filters it's important to have a long enough exposure. The other things to consider are number of autofocus steps and step size. Although
this video talks about SGPro autofocus, the theory is the same for all apps and might help.
Kevin