Procedural fairings works fine, you can re-intall it if you like. If I may wager a guess, your problem may have come from installing the mod "Procedural fairing for everything". It essentially makes all fairing bases (stock and modded) to use the procedural fairings interface and fairing parts, among other things.
A little while ago, I found out that one of the making history missions was unvailable, because the part "fairingside2" (or sth like that) was missing. Turned out that uninstalling said mod fixed my problem. Not sure of course if the mod was at fault, or simply I installed it wrong.
Dante80's post in Issue with Stock Fairing Contract and Mods was marked as the answer