The other thought I had was that maybe it was dust particles on the bulb itself .... not sure if that would produce a similar effect on the screen? I would think that if dust was the culprit, it would not be permanent, but these markings do not seem to ever change from day to day...
I just acquired a Samsung HL-R5667W DLP set and today noticed (never really saw this previously) that there are 4 or 5 small dark flecks that appear to be coming from the inside of the screen. Most of them are tiny, barely noticeable, but one looks more enlongated, maybe 1/8 of an inch...