I have had a complete scramble of my doubloon order happen at least 4 times (in all cases with at least 3 pages of doubloons). Each time I have been unable to reliably re-create it. This last time (by chance) is the closest I've come to a repeatable set of steps.
I very carefully arranged my 3 pages of doubloons (54 in all) in ascending order level, from Treasure Bath/Crit Boost to Level 65. Remembering all the past problems with power order, I then jumped to Avery's Court and "touched" the life fountain, exited the game completely and re-entered, and clicked my heels together 3 times (ok maybe I made up that last bit). I then swapped two adjacent doubloons on the 3rd page, closed and reopened my doubloon list, and voila! Instant totally scrambled doubloons. The first two doubloons are still correct, but there is no discernable pattern to the rest of the list. Incidentally, when I get in this state, I cannot permanently discard any doubloons in combat - they keep coming back later in the fight.
On a possibly related note, I am all but certain that doubloon priority is broken. It is hard to be sure because of the somewhat random nature of things, but I've had my top doubloons turn up almost last on several occasions, and the order in which doubloons appear looks suspect. I'm not sure if a) the actual priority is completely random, b) the actual order is the reverse of the displayed priorties, or c) the linked list screwiness causes the displayed order to have no relationship to the actual priorities. Given the scramble behavior, I lean towards c.