Combining scenes in Storyline

I guess we start at the storage location. If these were not on your hard drive, there can be some corruption from other storage places. Artiulate has stated the files should be stored on your computer. 

Next, did you use the exact same template for each. I normally start one project (scene) then save it with different names. Most of the time that keeps it straight.   

The best way is to build each scene in the same project and add them together within one project. I just adding scenes as I need them. 

In all the years I have been using the program I still find these little and sometimes big glitches that pop up. Again, the big one is storage. Save to your hard drive, this may be hard with a lot of companies wanting us to use cloud-based storage, but it prevents a lot of these issues.

Good luck