finally someone is also having the same problem which I am at my wits end trying to rectify but failed. My e36 have that "duk duk" sound every once in a while and each time I took the car to the mech the blardy sound seemed to miraculously disappear... only to come out again after I leave the mechanic. At first I thought it was the flap opening and closing but even when I put the aircond on circulating and non-circulating mode, the sound is still there. Also sent my car to Naidu (the aircond fella in PJ) and he confirmed that the aircond gas is still adequate.
I have learnt to live with that irritating sound all these times, but if someone can really pin-point the root of the problem to eliminate the sound alltogether, it would be excellent.