I would suggest simply turning off the Auto-save feature. If you are getting the lag about every 30 min or so, then the setting for auto-save might be at 30 min intervals. Turn it off and the lag will go away. Just be sure to save frequently, like say before going into a battle or high risk areas.
THiS is if you are on a PS3 though.
Also, Auto-save can create like 3-4 separate files of it's own... and that is on top of say the 1-2 manual saves you might have.
Make a save file manually, note that it is actually there and saved.... and delete all other save files. Start fresh with that last save you did. SHould result in noticeable changes. But remember again.... you HAVE to make manual saves on your own... or might find yourself about 3 days back for example than where you are presently.