yeah that was an issue with the KEA download on my server, which has been fixed.
let me know if you get word on the blank listboxes in the various tabs. also about the session thing and/or if this was a fresh load. also do the boxes populate in config > custom apps? if so see what happens when you add an app to a tab if it (and only it) appears or if the boxes are still completely blank.
another thing to check is using the d7II Main menu > Debugging > View/Modify Session Data open your d7II Config dir (I always say do it from there due to the portability of the folders and session stuff so you know you're looking in the right spot) and open the SortOrder folder, then any one of the cfg files for the custom boxes can be opened with notepad.exe -- see if for example your malware1.cfg (the left box on the malware tab) has any entries in it. would look like:
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33|1|32|6|9|10|my custom app name|18|12|13|16|17|8|7|
where numbers represent d7II internal function identifiers, and custom apps will just have the name in there. If these files are blank then your config just isn't there for some reason, but if they have numbers/names in them then I definitely have an issue populating the listboxes with the config files...