Thats exactly my issue! I flew her into a freking cave and now the doors are wacked and she wont move!

Same problem, landed in Mara's Eye Den, then nothing happens when I press the dematerialization primer.

Had an idea to fix this; try updating to SKSE 1.7.2, haven't tried it yet, but it might work.

If that doesn't work, try doing that AND downloading Nexus version. If THAT doesn't work, no idea.

I found out how to fixer it right up! Firstly you must have SKSE 1.7.2 OR 1.7.3, SkyUI and then the following! When entering the TARDIS, press caps so you (trust me) walk to the console, then press the dematerialization and walk around to the Nav Computer (walking around there is the time it takes for the quest to start) WARNING only hit the dematerialization ONCE and then WAIT for the quest to hit the Nav! Hit the Nav, choose say civilization, hit tab, and wait for it to open again! Only pull the handbrake once you start typing into the computer and the quest finishes, then you know the rest. Quicksave (F5) each time you exit the tardis. The ultimate thing is that this mod NEEDS patience! Do NOT hit the Nav before the dematierialization and if you want a random location don't mess with the Nav! If you rapidly click the dematieralization or hit the Nav before your supposed to, it'll get confused and stop working. I now use the TARDIS CONSTANTLY, but I'm patient, I quicksave, and if the Nav stops working or the dematierilization stops working I reload my last quick outside the TARDIS and I haven't had to do it once since I started using it properly, don't get angry with her, or try to understand why the Urial room is a consol room, just know that this is a new mod, that requires four things and rejoice in the fact this TARDIS has six buttons instead of three billion like the last tardis and if you press the wrong one, you don't end up in the bottom of the ocean or in the side of a mountain. It's a five star mod but it needs improvement! Remeber! If you think theres a bug or issue! Report it!!! :D

Or do what I did, just update SKSE, get Nexus version, if there's an issue, uninstall and reinstall.
That works too.