Yeah. The tutorials are really written for a pristine system, and you seem to already have these modifications. Could you possibly already have them checked in the document you are starting with? (Have a look in Peptide Settings - Modifications.) I guess it would probably be better for Skyline to show all the modifications it sees that are already available and just show them already checked. But, since that can't happen in time for the course, you should try the following 2 things in this order to see which one you would need to get the tutorial working as expected.
- On the Settings menu, click Default (probably No about saving your current settings)
- On the Tools menu, click Options. Choose the Miscellaneous tab, click the Clear All Saved Settings button. Restart Skyline.
Hopefully, the first option will be enough, but the second really should be, since it will essentially set you back to a pristine installation.