Sorry I missed this thread.
I just did a quick test on Factorio version 1.1.101, and everything seems to be working fine with long days and nights. I didn't let it sit for the whole hour, but the 10 minutes one seemed to work fine, and the hour one has been going for a while with no apparent issues. I even tried setting it to 999999 seconds and the days seemed to behave properly.
If anyone's still having this issue, if you can, please post an example save, as well as letting me know what Factorio version it's happening on. It might take me a while to get to since I have the willpower of a goldfish, but if someone's got a save where it happens or a reproducible setup for it, I'll definitely see about getting this fixed.