What do you mean it doesn't work with GMM? The manager crashes, or the game?
edit: this could be the same as electricz0ltan's problem right above your post, just check the "don't check if already present" box when exporting, should fix it.
As for directories, you're just loading them wrong; you have to point the editor to the exact folder that contains the blueprints and autoBlueprints files.
I guess that now I really have to write some sort of guide.
@Weltall Zero
You're raising very good points. I have been planning to change it, so that a window pops up at the start of the program, asking to point it to directories, should they seem to be missing, so that you can't omit that step. Or perhaps automatically scanning to find the correct folder... Or just loading data straight from the .dat archives (though I'd need to get some understanding of their structure first)
I've stumbled upon the Preferences class several times during my voyages with google, though I never gave it much thought... I suppose it's worth to take a look, though it's a farily low priority with all those bugs around.
As for NPE's, yeah, I mostly end up not catching them and instead creating a lot of != null if-checks. Though I guess you're right, catching the exceptions allows to easily identify the error, print out relevant message - without crashing the app.
Old habits die hard.
And you're not being rude - I'm not exactly the most experienced programmer out there, so any and every piece of advice is precious and really appreciated

As for your problem, that's simply image dimension issue - the floor image has to have the exact same dimensions as the hull image, and the cloak image has to be 20px wider and higher (that's how FTL is programmed). Take a look at default images, guess it'll be easier to understand that way, rather than me attempting to describe it.