Flats not eliminating all defects?

[BlueAstra]

I wonder if someone could give me advice. I have an original sub, which when expanded shows the faint dirt and smears in the system. My master flat also shows the smears. When I integrate all the subs with the master flat using the batch preprocessing script in PixInsight (default settings and a master flat) I still get traces of the defects (I also use a master bias, but no dark with my SX-H16 CCD camera). This also happens with DSS, but to a lesser extent. I believe the flat has a full histogram and mid value ADU. Any advice on why this could be happening?

[Singlin]

This might be a stupid question but are you sure that the Flats are recent?

[BlueAstra]

29 minutes ago, Singlin said:

This might be a stupid question but are you sure that the Flats are recent?

They are a little old, but I think the defects shown on the flats match the defects seen faintly on the subs.

[scotty38]

I don't know what the answer is but if you look at the calibration diagram in PI I assume the masters are being applied as you'd expect?