A thick dust grain on the CCD window can easily cause 1% absorption of the background light. In principle these effects will flatfield out, but as the JKT is rather sensitive to flexure, the image on the detector of the dust grains might shift a little as a function of telescope position.
Standard practice is that ING staff cleans the filters and the CCD window at the start of each observing run. If, during your run, you find that dust has accumulated to unacceptable levels, please submit a fault report asking for the appropriate optical surface to be cleaned.