To remove a square-taper crank, the full procedure:
When you screw in the puller, be sure that the "plunger" - the inner screw - doesn't bottom on the axle before the outer screw bottoms in its hole. If it does, it will feel like the puller is all the way in, but it may not have more than a few threads.
When pulling square-taper cranks:
- Visually inspect the crank, checking that there isn't a washer in the hole or parts of the dust cap still in the crank threads.
- Always screw the plunger all the way out before inserting the puller.
- Don't use a wrench to set the puller in the crank unless necessary. If you can't get it in with your fingers, then something is wrong (usually, the threads are damaged). You can use the wrench when you think it's finally all the way in to be sure it isn't hung up, or to force it past damaged threads but be sure it's not crossthreading.
- Count the number of turns the puller makes when inserting it. That will tell you how many threads are engaged. Anything less than about 6 and you're taking a risk.
- If the plunger is tight and the crank doesn't want to come off, tap the end of the plunger with a metal hammer a couple times. The vibrations should cause the crank to loosen. It may pop loose, or loosen just a bit. If it doesn't pop loose, try turning the plunger again to take up any new slack and repeat.