I have received a few questions recently about problems with the PowerPoint pen tool not working during a slide show
I guess somewhere out there, a teaching lesson using this tool had been going on, because I thought it was unusual to receive more than one question on a tool like this.
So, to that end I wrote about why this might be happening and the fix(es) for it. The problems differ between PowerPoint 2003 and later versions. Here are some articles that may help you out.