Well, I have been having a similar problem. I have mapped all of the axes, and I have been able to get my collective to work with this same joystick model X-45, by putting it on Slider 1, but the Throttle (The RPM Governer that actually controls the RPM), doesn't seem to be working right since I downloaded the patch. I can't adjust the throttle with the slider button on the throttle-stick now for some reason, so I'm trying to get the throttle slider to work again, but it's just not responding.
Also, the pedals I have, are two axes in and of themselves, so they aren't the 1-axis rotation that the Saitek makes, but they are the CH pedals with two pedals that operate independently of eachother. Those I haven't been able to get work on BlackShark EVER. And I've tried pretty much all 8 of the slider switches it gives me on the controls screen