If you could somehow copy every mod you have in here, such as copy and paste them or something, I could look into them for possible problems for you.
Other thing you may want to do is reload to a previous part of that same Quest and do it again and see if the outcome is the same.
(Another thing, you may as well check on the Fallout Wikia in the "Come Fly With Me" page, there is a part that says Bugs.
Read it as it explains any possible bugs that happen, look on the left of them for in wich versions of the game it happens and it explains how they happen and how to fix them/bypass them.)
If you do still receive the XP and stuff for completing the quest, them your bug may be the Second one of that list, that starts as: "No cut scene glitch:..."
Hope I helped somehow!