Interesting, I have made similar observations. Not with so much variation on the weights, but I do see little correlation between what I consider a good subexposure (low fwhm, low background level, nice shaped stars, etc.) and the weighting factors.
Are the weights determined from noise estimates, or from SNR estimtes?
BTW, another observation is that the batch processing script doesn't seem to pick the user selected reference sub at the integration step. Don't know what happens at the registration step, if it uses or not the right frame.
best
Ignacio