Any mods that change settings outside GameData?

[Geonovast]

I've run into an interesting problem.  I've been running a new shuttle program in my main modded install.  I switch between installs by changing GameData folder names.  Everything else is run the same.

I decided to run my SSTO I built awhile back, since I know it works and would do exactly what I needed it to.  Except it didn't.  I've launched this plane in previous saves many, many times.  Always gets to orbit with a minimum of 600m/s dV left.  Got me my K Prize.  I always fly it the same way.  But this time, it barely made it to orbit by using every bit of fuel.  Major difference I saw was acceleration, previously it always started slowing down on just the whiplashes at about 1350 m/s.  This time it barely hits 1100, and I have to hit the LF/OX engine early, using up all the fuel.

Thinking it was one of my more recently installed mods, I went back to my stock GameData folder (well, with KER).  Same result.  Could just not do it.

So then I did a fresh install, and only installed KER.  Grabbed the craft file from the save I was in, loaded up.  Acted normally!  Got to 1350 m/s just fine in the same amount of time I was used to.

What could be going on?  The Physics.cfg files between the two installs are identical. (Checked using the Linux diff tool).  Settings.cfg files are different, but I don't see anything that could be doing anything.  Just joystick config and brightness settings and whatnot.

Here are the mods I have installed in my main modded GameData folder.

I can do videos of both launches if it'll help.  Also can get log files if they're needed.  I used to have SVE installed.