Why are you using different settings for GAIN? This should be a number that, along with OFFSET, should be established emprically for your imager, tested, and then it should be left alone unless you find that new results of the empirical tests suggest that the new data is better than the old data.
Craig Stark has an excellent article about setting GAIN and OFFSET - search for it on the internet.
I always advocate trying to run your imager at repeatable temperatures and to have taken Darks exposed to match your Lights and Flats. The other way to look at this issue is to decide on some common exposure times for your Lights and Flats and then you should always have Darks 'on file' to match these. For example I usually always expose either 300s or 600s subs, and these are always taken at a repeatable -15°C. So, I only need 300s and 600s Darks. For Flats, I get excellent results with 2s exposure times, so I keep a set 2s FlatDarks as well. I don't ever include Biases in my calibration data - I am using an imager that doesn't introduce bias noise that needs to be removed.
In your case, you have just complicated the whole process by using different Gains and Exposure times. Just remember to StarAlign before ImageIntegration (and to CFAdeBayer before StarAlign, if your imager needs this stage).
Hope this helps.