I don't think the sorting issue is specific to collections. The issue is more noticeable when sorting individual books by "Last Read." Even if the Kindle framework shows the "correct" time, when things get out of sync, the Linux timestamp function (on the files themselves) seems unable to determine the time since "epoch" (1/1/1970). As such, the recently opened ebook gets timestamped 1/1/1970 which, of course, causes that ebook to be improperly moved to the end of the "Last Read" list.
Users have been experiencing this issue since the first generation of the Kindle -- either from not syncing for long periods of time or from picking up incorrect time (or timezone) data from different cell towers.
My wireless is turned off most of the time and I was plagued with this issue until I made a point of turning my wireless on at least once a week and manually syncing.
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