If you are seeing that file open as a manual install then there is something amiss with your MO installation. No matter which setting you have for your plugins, internal or external fomod installer, that file always shows in my MO 1.3.3 install with its fomod scripted install.
Can I assume you updated to 1.3.3 over an existing 1.2.18?
If that is true you may need to do a bit of cleaning. There could be some remants of the previous install conflicting, though @Tannin did make the new installer clean out that stuff first.
At any rate, grab the latest MO full install archive, not the installer, and open it in your archive manager.
Open an explorer window with the MO installation.
Delete every folder and file that exists in the MO install AND in the MO archive. This is to ensure no leftovers from a previous install.
The files/folders that you should be removing are:
Everything else is either a setting you have made or the downloads, mods, profiles folders with your files in them.
Copy all the contents of the MO
Full install archive and the result will be a pristine 1.3.3 MO
install with all your settings and mods intact.
Try that mod installation again and if still doesn't work could you post all the relevant details into a bug report in the Bug Genie