The fact that your lights are blinking makes me think either a power issue (not enough juice for the USB ports?), or perhaps a short/break in either the usb port or the cables.
I have an X52, downloaded drivers from the website, use SST and some programming within AH, and didn't notice any problems immediately after the patch.
I'd have a close look at those cables and the connections to the stick (both the cable tying the throttle and stick together, and the usb cable) and to the USB port on your PC.