If you are SURE there isn't a washer in there (you looked inside and can plainly see the square-taper BB end inside without anything in the way) then it should come off.

Check to be sure you have the right crank remover or that it is set up correctly and you don't have the wrong end-piece on. Some crank pullers have two different removable ends that pivot. If you have the bigger end (used for ISIS or Octolink cranks) on the crank puller it isn't going to be pressing on the BB and instead on the inside of the crank arm -just like if you had a washer in there. The end of the crank puller should have a pushing-end that is no larger than the diameter of the BB spindle. Make sure you didn't break something off or leave a piece behind in the other crank when you took it off.

Also, lubricating the threads within your crank-puller tool helps a lot too by reducing the internal friction. Regular grease works very well here. Lubing the threads of this type of tool is a regular maintenance chore that should be performed every once in a while to ensure they don't bind up.

If everything is lining up and fitting correctly and you have so much tension on the puller threads that you are afraid your are going to strip them then a give the crank a few bops with a big rubber mallet. You aren't trying to "hit" the crank off but simply add in some high-frequency vibrations into the joint while the tool is loading the pieces with pressure. A light and steady tap-tap-tap will get the metal vibrating and this sometimes help get things moving. You can also help things along by spraying in some high-quality penetrating oil designed for seized things like this. There is a product called "freeze-off" that works pretty well in these types of situations.