Update:
There were some small issues that, combined together, was causing the reading issue in this edge case. (Edge case being that users tend to mark readings as known or unknown after studying it at least once).
I was able to confirm, in my testing, the following:
(Change) Reading was marked as known, but "unmarked" after a single question in the quiz (Just as you stated). This no longer happens.
(Change) There should be better linking between the dictionary and the listings in the term lists. However, there can be differences. This is actually a subject of discussion for the next version of the site, but here is what typically happens:
Dictionary entries can be different because some lists (specifically, the JLPT, textbook, and Kanji Kentei lists provided by renshuu) have recommended readings attached to them based on where that list came from. These recommendations live within the list, though, and may not be reflected in the dictionary. (For example, JLPT N4 might expect different readings for a kanji compared to a textbook where it is introduced in chapter 3 of the first volume).
Once you study a kanji character in a list, though, you start getting "hey, this users knows these readings" attached to your personal study profile, and that takes precedence over any list or dictionary entry. Now, the previous bug you mentioned was getting in the way of this somewhat, but it should be improved.
Please let me know about any other (or same) consistencies you notice in your usage of the site!