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The mystery continues...
May I ask, what is this sticky tape for? Maybe light is leaking through it?
I noticed that in the setup with the filter wheel, that part with sticky tape is in front of the filter, while in the setups without the wheel, sticky-tape segment is between the filter and CCD.
I still believe the patterns you mentioned are caused by some internal reflections.
EDIT: Sorry, missed the bit explain sticky tape. Here goes my theory...
Having a filter so far from the CCD is a bit unusual, I suggest bringing the filter closer to the CCD and see if that solves it.
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