A couple of thoughts...
* You may need to click on the option to re-align subs that have already been aligned.
* Your star alignment threshold might be okay for your second set of 17 subs, but not right for the first set of 9. One way to check would be to see how many stars get detected for one of the frames for your first set versus the second set - if it's substantially different, then that may be a problem. I've found that there's a sweet spot for the threshold - too high/low runs into alignment problems.
* This is obvious... but have you checked that all 26 subs have check boxes next to them (i.e. that they're all included in the stack)?
* Are you using dark/flats/bias calibration frames? It's important that these are generated properly... I've run into countless problems with alignment when they've been problematic. Poor flats has been my biggest problem - sometimes it stacks better without the flats included.
* Worst case scenario, you could stack the first set of 9 subs together, and split your second set of 17 into two separate sets of 9 frames. Stack the three sets of 9 separately, and then stack the three output TIFFs together to get your final result.
Hope that helps!
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