The 3 charges per hand theory doesn't appear to hold water either. From the provided log.
6/6 11:07:38.703 You hit Servant of Allistarj for 95. - OH
6/6 11:07:39.515 You crit Servant of Allistarj for 488. - MH
6/6 11:07:40.484 You gain Flurry.
6/6 11:07:41.203 You hit Servant of Allistarj for 102. - OH, 2.500 delay
6/6 11:07:41.703 You hit Servant of Allistarj for 261. - MH, 2.188 delay
6/6 11:07:43.437 You hit Servant of Allistarj for 106. - OH, 2.234 delay
6/6 11:07:43.750 You hit Servant of Allistarj for 281. - MH, 2.047 delay
6/6 11:07:44.109 Flurry fades from you.
6/6 11:07:46.031 You crit Servant of Allistarj for 206. - OH, 2.594 delay
6/6 11:07:46.546 You crit Servant of Allistarj for 539. - MH, 2.796 delay
4 swings in Flurry, 2 with each hand, all noticeably hasted. In this case the result is pretty consistent with Flurry lasting 3 autoswings; the buff was in fact queued for faiding after the OH hit at 43.437 and the last MH hit just got to tag along for the ride.
My best guess is that what you're looking at is the Flurry "stack" being both slow to renew to 3 after a crit mid-Flurry and slow to fade when it's supposed to. If you crit while at 1 charge remaining then the game takes a second of thinking time before getting you back up to 3 charges, so you get a free extension of your old Flurry. As a Flurry is expended the game takes a second of thinking time to actually fade it, giving another free extension. The two effects combine to make the tail end of any Flurry streak considerably longer than it has a right to.
A good way to discount the above possibility is find an isolated Flurry that lasts for 5-6 hits.