Linked Projects Not Saving Progress

I'm having a problem with a course not saving students' progress. I've built an 11 module course in Storyline 3 that is too big for our band width. So I've tried breaking it down into individual projects and adding a menu. I have the links working and it is set to save their progress. It is also set to ask them if they would like to resume when they return. But when the employees exit the course it does not save their progress. Has anyone ran into this issue before and if so what have you done?

I've tried setting the links to open the modules in the current window and in a new window. Neither will save the employees' progress and both seem to have their own issues. The current window won't update the menu and closes everything. The new window allows the user to click on the "x" in the upper right hand corner to close the window and return to the updated menu. The problem is it lets them bypass modules.

Sorry, everything in the course is proprietary so I'm unable to share.