Interesting.
As of a day or so ago, I'd been having some minor issues with playing "Speaking in Tongues" in the Tech Room, myself. (I'm running the recent "White Squares" 3.6.7 build, and only the FSPort for mods.) I assumed I just did something I wasn't supposed to("broke" something, somehow).
I was most of the way through the campaign in my current pilot, and after installing the latest version, I thought I'd go to the Tech Room and play one of my old favorite missions, "Love the Treason..." (mostly as it's one of the few campaign missions you can use a Herc I on). I restarted it a couple of times(due to Snipes dying, or the Hamako getting eaten by flak), then exited from the mission(ESC menu). I then wanted to see if the nebula performance was improved on this version, so I went to the last mission I was up to in the Tech Room, which was "Speaking in Tongues".
Things seemed normal at first, but when I got to the Ship Selection screen, the inventory icons on the ship list were missing, and I had a Herc I for myself and Lokis for my Alpha wingmen, plus Beta Wing was all Herc IIs. When I went to the Loadout screen, I found a drastically limited selection of weapons, and I believe I saw that I had the same default loadout set up as I'd had for "Love The Treason". I decided to play the mission regardless, and I completed it normally(albeit with my wings having the listed Terran fighters).
I loaded the mission again in the Tech Room, and found the same ship/loadout situation. I then checked my current campaign mission ship/loadout; everything was normal there, but "Speaking in Tongues" was still showing the odd ship/loadout setup. I tried playing "Love the Treason" all the way through(everything normal there, as well), to see if completing it might somehow cause the game to "unload" the apparent problem, but to no avail.
I tried restarting FSO to see if that cleared it. Nothing. By that point, I was tired of trying to fix the problem, and decided to just go play some more campaign missions and forget about it. I also ran a few other custom missions after that, which also ran normally.
Today, I decided to check "Speaking in Tongues" again to see if things were still off, and it appears the normal Vasudan ships and loadouts are back.