hook_form_alter - validation function does not get called in Internet Explorer
The Form API works via PHP and is executed in its entirety on the server. There really should be no question of browsers being involved in the equation. That is, unless you are doing something with JS (or CSS/anything client side) that might affect form input.

I would:


Clear all my caches.
Ensure that I'm working on the same page, site (and as the same user) in both FF and IE.
When you mention "printing the $form info", I assume that you are using the Devel module. If you aren't, you should be. Devel's dpm() function is the best way to debug these things by adding diagnostic print statements in each step - the form, the validation hook and the submit hook.