Hi Marcin,
That's a bug in BigBlueButton's whiteboard. It's intermittent and we've not had a sequence of steps to reliably reproduce.
At the moment is a low-priority bug as the whiteboard marks that linger are only visible to the presenter.
Still, we want to fix it, but it likely won't happen in BigBlueButton 0.8 as our priority is to finish the record and playback capabilities.
Here's a link to this whiteboard bug in our issue tracker.
Of course, you don't have to wait until we fix it ... if you like BigBlueButton and want to help, this would be a good bug to try and resolve if you have some programming skills.
Regards,... Fred
BigBlueButton Developer