Make sure that you don't have any JS buttons mapped in AH's setup, that are in use by the x45 profile. (They cancel each other).
(in reading your post, I believe you've done that:))
Next, Make sure that your profiler is loaded and working in windows. (ex: Icon appears on the sys tray as active, and the js shows up in the windows "Gaming Options", and works).
If the above is good; Then open the AH JS calibration window, > 'select JS' , and see what buttons and knobs are functioning there.
I'm using an SWF22 now, But when I had X36's and X45's, Any buttons/knobs that were covered by my [active] profile, were not mappable in the AH configurator.
Hope this helps;