BigJoe.....same stick here and had the same problem a couple of times. I also use the CTFJ ver 3.20 from
www.stickworks.com I cal'd in AH....had same prob, so I exited, rebooted, (MS PPFF recals auto in W98 on startup). I checked cal in W98, it checked ok, then started the CTFJ. Then in AH I checked the joystick settings, but did not recal in AH again. Recal'g in AH seems to throw my stick out of whack. (just full of tech terms aren't I). With the w98 recal and the CTFJ I'm not having many stick probs, just can't fly for crapola
I'm probably not much help here, but thought I'd add my .02 cents worth anyway.