I've narrowed it down to LookingGlass. Without LookingGlass everything is just fine.
I'll let the images describe it better than I can. However I will say this I'm going back and forth between to books that are intra-linking books.
Also note that the Crystal Growth Accelerator shows as being offline but I can still access the ME drive and the stuff on the drive while also the storage cell looks like it's missing.

This is normal:
http://i.imgur.com/8Xobvvw.png and http://i.imgur.com/2JnXaNB.png

This is what happens going from 1 book to the other and back:
http://i.imgur.com/2JnXaNB.png
http://i.imgur.com/2JnXaNB.png

Here you can see that the cables are not connected to anything so the accelerator is offline
http://i.imgur.com/TBMofox.png
and yet I can still access the drive at the other end

Here you can see that the storage cell is missing, which you can barely make out was there in the first image
http://i.imgur.com/i2cNOZZ.png

And lastly this is what looking glass is shows me
http://i.imgur.com/QQFhnRZ.png

Has to do with how LG is handling TEs at the moment... I'll look into how best to fix this.