The cable between the JS and throttle is likely the culprit!
If you dont have the X52 fastened down then you need to secure the cable,I used a small loop and some duct tape and taped the cable to the base of the throttle and the base of the JS. It''s a PS2 cable and doesnt fit all that great so I took some Cclip plyers and spread the outter ring of the plug to make it fit abit more snug.
Eventually I mounted my X52 and used cable hold downs to secure the cable. Once the cable was secure I never had the lights flash after that and seldom ever had to calibrate. I used a powered hub from the start so I knew it wasnt an issue with power but if I even touched the cable just alittle it would cause the lights to blink!
Also while your at it check to see none of the pins are bent or loose,as that could cause the issue and is usually caused by the loose cable to begin with. Good news is all you need do is pick up a new PS2 cable and Bob's ur uncle!!
YMMV.