Tamihana,
Thank you for trying MyEclipse 2016 CI 3. We do not see the issue with shortcuts at our end.
After restoring the keys in the General > Keys preferences page, can you please restart MyEclipse and check if it fixes the issue. Can you also check if the issue persists in a new workspace as well?
It might be possible that there are duplicates bindings due to plugins defining some of the keys. Duplicates can be checked by sorting on the key combination, making duplicates easier to see. If there are duplicates then please try other shortcuts that use the command key.
Apologies for inconvenience caused. Let us know how it works for you.
–Swapna
MyEclipse Support