Hi Mario,
I havent heard of this happening before. I do know that ie6 can get a little cranky with some javascripts but generally not the mootools file itself.
Is this happening in J1.5? If so then you can prevent the file from being loaded automatically if you are not suing mootools. Otherwise you could download a fresh version of mootools and then see if that has the same effect.
I guess the main thing I need to know is what
template are you using? which version of Joomla and are you using any thing that needs mootools.
Cheers Anthony