Your main account does not have the checkboxes for calendar and contacts, as they are synced automatically and this can't be changed.
However, I am currently having a problem with my contacts not actually syncing, which is probably what you have too.
EDIT
Got mine working.
I don't know if anything I did helped, but my after resetting my phone last night my Hotmail contacts were not synced after ~12 hours. I did a few things to try to force a sync, and I don't know which (if any) did the trick, but my contacts are now syncing (but very slowly...it's like one contact syncs every half hour or so).
Here's the things I did:
created a new contact via Outlook.com
changed a contact details via Outlook.com
changed sync to 15 minutes
rebooted the phone
A few of my contacts have now synced, and I think if I wait for several hours they will all eventually sync.