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OneDrive for Business has a number of limitations on what it is able to sync. See the list at OneDrive for Business - Sync Restrictions
FAQ
Should I move all of my files into my OneDrive Folder?
Your storage provided by CSCS - your Home drive and Group drives - offer more reliable backup than OneDrive for Business, so you should not move everything in by default. We recommend using OneDrive only for files that you create or use offsite.
When I enter my credentials into the sync client, why do I get asked for my 'Microsoft Account'
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If you enter a personal, rather than academic email account, you will see the following credentials prompt:
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