It appears as though the upgrade to MacOSX 10.13 creates some problems for AIJ, which may be mosty generic ImageJ problems. I don't have a complete list by any means, but the most important one (and it's common to generic ImageJ, as well) is that the user can't type in values into dialogue boxes (e.g., when importing a stack of images, specifying the number of images to load (a generic ImageJ function - the same issue appears in generic imageJ, as well - on at least one Mac that upgraded to 10.13, the command menu - File/Edit/View.... didn't appear!) When I checked with a couple of AIJ-specific dialogues (the data reduction facility) I successfully could input values, but when I tried it with the "Set SIMBAD search radius" I was not able to alter the default values.
FYI, upgrading to the most current generic ImageJ version (1.51q) does NOT fix this problem. The ImageJ2 version I had installed also experiences this compatibility issue, and on the ImageJ2 homepage it indicates it can't be upgraded to the current Java 8. However, (and it was a life-saver!) Fiji appears to work fine (so far at least!).
I tried the steps you suggested, including doing them after a clean install, and it didn't seem to fix the issue of being able to select and type values into various dialogue boxes (e.g. the "Analyze / Multi-Aperture..." dialogue.) However, I CAN change values via the sliders in the Multi-Aperture dialogue (as I could before trying your suggestion).
There seems to some conversations on-line about ImageJ not running well on MacOS 10.13 in general - including missing the menu of commands (one of my students ran into the missing menu issue - I didn't, but did experience the typing-in-dialogue issue).
As I reported in a different place in the forum, I have found a work-around for not being able to type into dialogue boxes. It appears that about the only input mode that doesn't work is via the keyboard - the track pad / mouse allows one to drag and select, click on buttons, drag sliders, and so forth. Thus it's possible to type the desired values into TextEdit, copy the value, and paste it into the dialogue box.