I remember someone having the same issue before, where he had an unusual high negativ amount of faith and thus it would've taken forever to get to a normal amount again. I think back then I changed the system so that if you go below 0 it'll automatically bring you back to 0. This way you should be able to always get up to 100 as long as your gain isn't negative.
If you've already tried to change your policies and wait for a longer periode of time (real time as long as the game is running! Not warmap turns, steps, battles, times you sleep in the bed or anything like that.) and your issue is still not fixed you can send me your save file to Naughty-Netherpunch@web.de and I can correct those variables.
Faith has no effect in the game at the moment.