Mine did this a few months ago. Loud 'thwunk' sound at 2-3 second intervals from the vents, fading out after a few minutes use. I made an appointment to see my tech, and the sounds stopped before I could get in. It only did it for 5 or 6 days total. He said there were a number of doors and vacuum components in the AC system which could be responsible, but if it wasn't doing the noise right then, he wouldn't go into the dash, and suggested waiting until something got noisey again or stopped working. Of course it hasn't had a problem since!
2003 Firemist Red/grey leather SL 500
2015 Palladium Silver/black mbtex GLK 350
1987 Smoke Silver/burgundy mbtex 300E Sportline (SOLD)
Click to see 87 300E