I just noticed when attempting to compare players, and you go to select the option to use your shortlisted players, it will only work with players on your "Default" shortlist. If you have other shortlists, it won't let you select them.
Here's the screen:
https://cloudup.com/cX4PaVvdUHe
Please give us access to all our shortlists when wanting to use them for comparing players. It would be massively helpful!