I think some of the problems are due to the default profile not being properly purged, which is causing unexpected behaviour. The file is called SAID075C.pr0 on the X52, and I think is in System32. Perhaps just getting rid of it would do the trick (move it, don't delete it, so it should be reversible).
My solution was trying to uninstall and reinstall the drivers, which was a faff and didn't work properly. By good luck it seemed to kill the need for profiles (I don't have the SST software installed anymore), but still allowed the use of the mouse functionally on the throttle, which is all you actually need from the drivers for Elite.
At various times I've had the flashing buttons issue, the pinky trigger issue, and the 'Mo' issue! All I can say is, Saitek have really crappy drivers, and >100mb for the SST software is ridiculous. Shame, because it's a good stick otherwise.