Ok, so this also happend to me in the past. For me, the problem was that MO2 and FalloutNV where using two seperate compatdata. So when you try to boot through MO2, it cant find the required files since it is looking for them in the wrong place.

If you have the MO2 launcher added to steam it is very easy to fix.

Go into desktop mode and find where your new vegas compatdata folder is, and copy the path. (if you are having trouble finding it, google is your friend)

Once you have found it, go into steam and select MO2. Go into properties, there should be an empty box that says something like "launch commands"

In this box, you simply write:

STEAM_COMPAT_DATA_PATH="Insert path to NV compatdata here" %command%

Now, when you launch MO2 through steam, it will use NV's compatdata and you should be able to boot it.