Hi Hobbit,
Sounds like you're doing everything right! However, keep in mind that AutoDev is just the start of your processing and any stretching you perform merely acts as a visual aid for you to see what you're doing (in StarTools you redo your stretching as many times as you like).
AutoDev in particular will help you find issues in your data, since it creates a stretch that is optimised to show every little detail - warts and all.
Without seeing what you end up with after the initial AutoDev, chances are it will highlight stacking artifacts, dust donuts, color bias, light pollution, gradients, dead pixels, etc.
Deal with these issues one-by-one and after dealing with each, re-stretch. You will get closer and closer to a 'clean' data set upon which you can base your 'real' post-processing, including your 'real' global stretch (for which I exclusively use AutoDev these days).
If you can't figure things out, shoot over your data (Dropbox or similar) and I'll do you a personalised tutorial. In the meantime also have a look at the
YouTube video where M33 is processed from LRGB data - it should deal with very similar issues.