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Hi Justin, we've not had many time out issues but I am aware of the time out set up in Cornerstone, having discussed this with of our 'Jedi Master' Admin users. The time out for Cornerstone is set about 4 hours, and even if someone leaves a course open in the background all day, when it auto logs them out it will ping back their progress at that point in time so will send something back to their learning records.

One area where we've had issues with tracking properly is when users have had more than 1 window open at the same time. If they part complete a course and close down the windows the 2nd closed window will override the progress from the 1st window/version and affect the progress. All cases I've investigated were users doing this and not knowing in some cases they had got multiple windows open. Not sure if this may be the case for you, but thought I'd share in case if was worth investigating as another possible cause.