[bojan]

Never had ANY issue or problem with DSS..
Your problem might be in background calibration.
The calibration should be "Per Channel Background Calibration", and not "RGB". RGB is perhaps more appropriate for dark skies, while it will seriously twist colours taken from light polluted areas.
The setting is available at the bottom of the "Light" tab in Settings.

Also, for final tweaking (including colour boost) I am using DPP (from Canon, it comes with camera).
I had a post on this forum earlier this year, describing the whole procedure.

EDIT:
I am using tiff format as output from DSS and input into DPP, for final tweaking.