I found the problem! Vortex is messing up the plugin.txt file. After restoring the file to the original load order of the base ESP, there were no more issues. So Uninstall all the mods in Vortex. Then delete all the lines in the plugins.txt file and copy in the original load order. After that, you can reinstall the mods through Vortex without any issues.
The correct load order is as follows:
Oblivion.esm
DLCBattlehornCastle.esp
DLCFrostcrag.esp
DLCHorseArmor.esp
DLCMehrunesRazor.esp
DLCOrrery.esp
DLCShiveringIsles.esp
DLCSpellTomes.esp
DLCThievesDen.esp
DLCVileLair.esp
Knights.esp
AltarESPMain.esp
AltarDeluxe.esp
AltarESPLocal.esp