DSLRs tend to make auto aperture adjustments in jumps rather than smoothly like a camcorder. I've noticed the same jumps in exposure from flip style cameras ( though in that case it must be electronic since the aperture is fixed to a constant size). I get around this on my Nikon by assigning a button to lock exposure and doing the extra step of locking the exposure each time I shoot. Once the footage is shot, there is no easy fix. It sounds like that is your problem. Do you know what camera was used on the footage?
I've got some very odd footage that I filmed on a Kodak Zi8 "flip" type HD video camera inside a winery in Napa/Sonoma Valley on a visit. It is a pulsing effect which I (think correctly) assume is to do with the fact that I was filming PAL (25 fps) and I assume the fluorescent lights were running at 60 MHz. It gives a very consistent weird, pulsing general strobing effect to the whole scene. Very noticeable. Happily, the video was purely mine, so didn't matter a bit.
Don't know if this is relevant, and I think there's been other posts on this forum over the past 18 months about fluorescent strobing, but I thought I'd let you know about this experience, perhaps it's relevant?
Is the light fluctuation akin to the flicker you see with old 8/16mm file captures? If so, johnmeyer has published some amazing AviSynth scripts to fix these issues. Search on johnmeyer & avisynth and/or flicker.
I use these all the time to fix my Dad's old 16mm footage:
It turns out Laurence was absolutely right. The aperture was set on automatic and would start adjusting now and again. I asked the guy to adjust the aperture manually before he started filming and it solved the problem immediately.
Thanks to all who made suggestions. I will take a look at AviSynth. It may end up being useful one of these days.