I did a bunch of flying yesterday in the Baron, Bonanza, and Caravan, and tested this in all three. I'm still having a similar issue: I was able to capture localizer but NOT glideslope after using the RNAV units -- the autopilot stayed in appr mode, and glideslope indicator appeared, but I flew right through it at the final approach fix in each test. In my final test, I tried recycling appr mode and it didn't help. I got the same behavior whether I used the appr mode on the RNAV units, or the KAP 140.
I do use Axis and Ohs for control binding, so sometime this week I'll test with default sim bindings (although I don't look forward to setting them up!). For today.. just gonna fly for fun.
I have yet to test with the KLN-90B.