Just want to say, that I had the same problems with FPOOS 17.10, coming from FPOOS 17.04 and thus switching from Android 5 to 6.
And I didn’t use Snooperstopper. The only thing I had to flash in addition to the ROM was Xposed to use Xprivacy.
Now after wiping and spending days to also install everything again from scratch on Lineage OS, I hope the only problems to deal with after updates will be easy to solve ones, as mentioned here today.
Of course it is helpful for this, that I won’t use Xposed anymore on Lineage OS as Xprivacy is not available and also not that much needed there as on FPOOS. And if this big update problem on FPOOS has nothing to do with Xposed and Xprivacy, it probably just was something with the permissions and the big step from Android 5 to 6.