I did some follow-up tests (for convenience, on Android) regarding the user dictionaries missing from custom groups upon restart and it seems it's not caused by an excessive number of user dictionaries installed.
First, I assumed MoEDict to be the main culprit since it's significantly larger but removing it didn't resolve the issue. Then I entertained the possibility that it's something wrong with my regenerated AV Chinese dictionary: the previous version populated on Android was 3.14 MiB in size, while the new one, created on iOS, ended up being 3.33 MiB despite not having anything added (in fact I removed one duplicate entry and fixed duplicate quotation marks in 58 defintions, so, holding all else constant, the file should be smaller). I disabled the full-text search index, to no change, and finally removed the dictionary altogether.
My third guess was the flashcards database, which got somewhat large, so I erased it as well (using the menu function). No change here either. Finally, I removed all the user dictionaries and with an empty flashcard database added the smallest of them all, Radicals-120605 (212 KiB). Whether the dictionary is copied manually to /sdcard/Android/data/com.pleco.chinesesystem/files/databases/ or I use the menu option to install it, the issue is still there. Also, I've been able to reproduce the all-empty entry on the dictionary list, and took a screenshot of it (attached). It happens when the new dictionary (Radicals in this case) is added, and appears on the bottom of the list, after I drag it up.
Another thing I noticed is that when there are no *.pqb files whatsoever, Pleco takes less than a second to start up, whereas as soon as there is any .pqb file present it spends as much as 3 seconds on the grey background before the interface appears.
It really looks as if there is (are) some ghost dictionary entries or other settings that cause this problem and they persist despite the settings being reset (tried that again just a moment ago, also repeated the final attempt with the AV Chinese dictionary instead of the Radicals). I'll now wipe all the Pleco data from /sdcard/Android/data/com.pleco.chinesesystem/* uninstall the app completely and install it again, and I have a hunch this will solve the problem (will update the post) but would like to know what caused it in the first place, if anything so that I don't do it again. Hope the above helps with debugging, it's possible the original fix you had in mind (increasing the timeout) might not be necessary at all.