1) Clean your film and the entire projector. Get all the dirt out of it and make sure all the nuts, blots and screws are in place and properly tightened.
2) Replace the drive belts on the back of the projector but make sure you clean out all the black junk built up in there. Again, make sure everything's tightened properly. Also check the alignment of the pulleys.
I'll explain more later...
Josh
A "thumping" or "whooshing" sound with an analog soundtrack could be due to a soundtrack application (silver redevelopment) problem. A motorboating or "putt-putt-putt" sound could be due to misalignment of the analog sound reader, or sprocket runoff damage to the print.
Do the sound problems remain constant through the trailers and feature? If so, it it more likely the equipment/alignment than the film itself.
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John P. Pytlak, Senior Technical Specialist
Worldwide Technical Services, Entertainment Imaging
Research Labs, Building 69, Room 7525A
Rochester, New York, 14650-1922 USA
Tel: +1 585 477 5325 Cell: +1 585 781 4036 Fax: +1 585 722 7243
e-mail: john.pytlak@kodak.com
Web site: http://www.kodak.com/go/motion
When I was working on a problem that sounded similar to this I found that the drive belts (Simplex PR-1050+5 Star) had become worn out and they were transmitting vibration through to the cell.
Replacing the belts and cleaning out all the gunk solved the problem. Realigning the pulleys made sure it didn't happen again.
Mine happened when I had been only working as a projectionist for about a year....so I just stopped after I added the thing behind the cell.
)Another one that has bitten me in the ass a couple of times is worn out bearings on the impedance drum shaft. When this happens you'll get either a grinding noise like an old washing machine or a warble caused by uneven rotation of the drum. Again, replacing the worn/damaged parts and making sure the alignment of parts is correct will make sure it doesn't happen again.
The "trick" is getting somebody to believe you!
My boss (who was a corporate manager, not a technician) didn't believe me when I told him that this was a problem. I had to get him into the theatre and demonstrate it to him in person. The machine had been repaired so there was no extraneous sound coming though the system. When I took a screwdriver and tapped on one of the pulleys it made a ringing sound, clear as a bell. Even with the sound turned on but the projector turned off you could still hear it!
If your projector has the CCD/LED reader this will be a lot less of a problem. However if you still have a solar cell/exciter you will always have this problem to some degree. If you have a JaxLight in your projector you will get it REALLY bad! The preamp they make you install in the solar cell line has so much gain that it picks up every little vibration in the system. It's so bad that if your drive belts are frayed even a little bit you'll hear this little "Ping-ity Ping-Ping!" sound caused by the little frayed strands as they hit the flanges of the pulley as they fly by. It sounds like a mixture of static ("Frying eggs" sound) and a ringing sound.
I sat in front of that projector for 3 or 4 hours just staring at it as it ran trying to figure that one out! I had been there all damn night long since at least midnite. I didn't get it completely solved till about 7 or 8 in the morning. 
Thus, the reason I said change your belts, clean out all the gunk and make sure your pulleys are perfectly aligned, lest the edges of the belts get frayed again in a short time.
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So if old projectionists don't die, what happens when new projectionists get old?