To fix the MCI error, close the game, open a terminal and delete the following videos (only ever played when the game starts... they are irrelevant):

rm ~/.steam/steam/steamapps/common/Flashpoint\ Campaigns\ Red\ Storm/Libraries/Animations/*.wmv

Problems:

1. Cannot use arrow keys to scroll the map (makes setting long waypoints a pain)
2. Mouse cursor occasionally gets "stuck" dragging the map requiring another click to release it.
3. Some fonts are aliased (see: ugly)