I've got a couple mods installed, but none effect base missions (or so I think). The bug occurs when the map loads up. Instead of loading proper assets, tile sets and objects are missing or have a translucent appearance to them. Over every area solid or semi solid white squares appear block the assets underneath them.
List of mods installed
Armour Resource Pack
Skitso's Map Pack (I don't remember downloading this one, but it was in the list so I activated it)
Cybernetic Armour
armoured Assault!
Dynamic UFos
Fire in the Hole
Hold the Line
Khali's Tundra Tileset
Radom Map Pack Artic, dessert and farm editions.
Fixed: Turned off Armor Resource Pack...Yeah I don't get this ether.