Youre likely recruiting in a high heresy region, which means the imam will spawn already susceptible to heresy with things like unorthodox and so forth. Then, you have other heretics and heresy in the region which converts your imam, and he joins the heresy side. This multiplies and becomes more and more powerful an effect the more heresy there is in a region and the more heretics you have about.

You likely encouraged the heresy and now it has snowballed into a real problem.

Its not the modded game, it's simply your misfortune on this particular campaign.