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Phil,
That's very interesting data, very nicely collected and analysed.
How sure are you the dips are caused by the zodiacal light & milky way? I'm not really convinced, nor am I convinced scattered light from Venus would affect the sky brightness at the SCP noticeably (but I could be wrong). If the data is taken in November, it could even be scattered sunlight since it gets dark quite late - true darkness sometimes does not occur until the Sun is 20 degrees below the horizon - the time at which it becomes dark being most dependent on aerosols in the atmosphere - more aerosols, more scattering, gets dark later. Could also be compounded with some diurnal airglow variation.
If you had the time, you could do photometry on a few stars in that region to obtain a calibration, and convert those pixel intensity values to mag/arcsec^2, which would quantify how large the variations really are. It would also be useful it you stated the field of view of that 100 px squared region (I can't be bothered to work it out...!)
Anyway - enough random thoughts and ramblings...
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