Unchecking mods may be useless, if whatever mod you have used for your facial textures and/or meshes has at least some of its effects stored in your save, as it apparently/probably has.
As this is most likely a mod issue, your best course of action could be to report it to the developer of the mod you have used, and hopefully he/she might be able to sort it out.
P.S.
Also note, that although I don't yet use mods like this with Skyrim so I have no experience about them, and this may not be your issue, my assumption would be, that once one starts a game with a facial mod, one sometimes may be tied to it for the duration. Meaning that it cannot be easily uninstalled or changed to another without running the risk of some anomalies. One way to resolve your issue might be to restore your setup to the exact condition it was in before any issues emerged, if there ever was such a condition.