It sounds like the tool is bottoming out. Flickerx, does the tool do the same thing if you were to screw the part with the arm all the way into the puller part (when it's not attached to the bike?)

If so.. add some shims between the end of your bottom bracket spindle and the plunger on the tool. A decently sized nut should do the trick.

I've had this problem before, although the crank arm was 90% of the way off before the tool bottomed out.