I have MJ 2.3.1 with KSP v24.2 and even though I have Mechjeb unlocked and I can place the parts, the interface box doesn't come up. Not sure if it got moved or hidden sometime in the last couple months as I haven't played in a while.

I have the same problem. I can control a vehicle with a mechjeb unit on it but have none of the dialogue boxes. MJ 2.3.1 KSP 0.24.2 Linux 64 bit. I tried full clean reinstalls, sandbox, unlocking all modules in the techtree in campaign... still nothing. Sure do miss a few of the modules, completing the tech tree gets tedious with out mechjeb.

So ... how are we supposed to help you ? Obviously MJ works for us so it's a bit hard to tell you what to do when you give not much more than "it does not work".
Without posting a log you won't get much help.

And for some reason it shows I have two separate but identical AR02 cases, one is unlocked but the other says it needs "entry purchase in R&D", so I go find it and unlock it, but when I get back to the VAB its still greyed out and a visit back to R&D shows the case unpurchased... like its stuck in some kind of vortex

As I'm still new to all this, I'm unsure how to get a log and/or post it

First find the log :
Windows: KSP_win\KSP_Data\output_log.txt for 32bit or KSP_win\KSP_Data_x64\output_log.txt for 64bit
Mac OSX: Open Console, on the left side of the window there is a menu that says 'files'. Scroll down the list and find the Unity drop down, under Unity there will be Player.log Aka Files>~/Library/Logs>Unity>Player.log
Linux: ~/.config/unity3d/Squad/Kerbal\ Space\ Program/Player.log

Then upload it on rapidshare, a public dir in dropbox or any other file sharing site.

For the no UI in Linux64 here is my log. I don't get multiple parts like tflo6.

https://dl.dropboxusercontent.com/u/49215029/Player.log

Thanks that worked like a charm. I used steam to delete all local data, but apparently the very old libraries were not deleted. I neglected to check the actual directory after deleting local data.

allenmaher you have 2 mechjeb dll, one very old :
Kerbal Space Program/GameData/MechJeb2/Plugins/MechJeb2.dll
Kerbal Space Program/GameData/Squad/Plugins/MechJeb2.dll

The 2nd one is a version 2.0.8.0, and is in a strange dir. You should not have a plugin directory under GameData/Squad.
If I were you I ll delete my whole gamedata, use steam to check the file and let it redownload it and then reinstall mymods.

Here's my log

https://dl.dropboxusercontent.com/u/52561339/output_log.txt

Same problem, you have 2 mechjeb...

Non platform assembly: C:\Program Files (x86)\Steam\steamapps\common\Kerbal Space Program\GameData\MechJeb2\Plugins\MechJeb2.dll (this message is harmless)
Non platform assembly: C:\Program Files (x86)\Steam\steamapps\common\Kerbal Space Program\Plugins\MechJeb2.dll (this message is harmless)

Delete anything in
C:\Program Files (x86)\Steam\steamapps\common\Kerbal Space Program\Plugins
and
C:\Program Files (x86)\Steam\steamapps\common\Kerbal Space Program\Parts

Mods don't use those anymore.

This worked wonderfully, thank you so much