This has been a long standing issue with codeigniter from what i recall, i remember having these problems in 1.7.X i believe? From what i've read previously it's down to a race condition although i'm not sure of the specifics, i've noticed it happens more often when you have regular ajax requests being made in the background, it is quite a big flaw for an application framework.
Have you tried setting the sessions so they do not expire or rotate the session ID, i've found this helps with the ajax+sessions issue although it's not really a good solution as it's not great from a security perspective to have sessions which never expire at all regardless of if the users browser is still pinging the server in the background or not.
If anyone has better info on this issue and how to work around it i would also be interested to hear of a better solution.
