So are you now saying LOOT doesn't even load? Even if it does start and shows the incorrect plugin list there should be a log to show this.
Are you sure you have no other software running that is interfering with MO's functionality, as per my link referred to earlier?
If there are none please try this. Uninstall both MO and LOOT and install away from your Steam library. Just place them in their own folders off the root directory, or off the "Games" folder. e.g. C:\Games\MO, C:\Games\LOOT