Calibration frame issue?

[smashing]

So managed the one clear night in 3 months the other day and thought, as there was no moon, i'd see what things were like without the L-Extreme filter on the 2600MC pro.  I managed to get about 40 mins on M51 made of 30 second exposures, things look ok until you start stretching things around but it soon becomes a bit of a mess.

Its a pretty quick stretch and level in PS and I know there are gradient issues but what are the red components? Are they issues with the flats? Maybe, being that it's been so long i've just messed up a step here.

[daz]

They look like shadows of dust from the flats?

What do the flats look like?