With particular respect to PR #130, could you make sure it's changing the tracking behaviour as documented in the pull request? If not, it may be that the patch hasn't been correctly applied* - or you're not getting it updated on the LMS (through not clearing browser cache, for example?).

This just seems like the most likely cause of the problem. Pretty much every course we build will have IE11 in spec and we've not seen anything else cause this sort of delay when restoring a course's tracking in IE11.

* it might help to turn on Adapt's SCORM debugger, which can be done using the _showDebugWindow setting.