I've done a quick test with 90/5 settings, and I think I have worked out what is probably causing the observed behavior (see attached map):
I generated about 25 systems before getting a loop, which was from System #4 to System #1. This loop was only generated after all systems with IDs within ±5 had been generated (999, 1000, 1, 2, 3, 5, 6, 7, 8, 9). My guess is that this is probably related to the change to prevent dead-end star maps, and I agree with Steve that he probably fixed it accidentally as there were a couple of bug reports which I recall were found to be related to that new code.
Steve reported getting a loop within 4 connections at 100% local chance, which imples the bug was fixed unless the settings were something like 100/2, so I would guess it is indeed fixed by accident.
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Side note: BUG REPORT
I got error #1654 in some cases when generating systems while doing these tests. Not sure if this is unique to Random Stars, but I don't recall seeing it in Real Stars games. I have all spoilers off, so it's not the error that happens when Rakhas generate sometimes.