On a fresh install of OS X Yosemite, the notes.app was unable to see the notes stored on my IMAP server. The account was working properly in Mail, and notes.app worked fine with other accounts.
I recall having this same problem with a previous version of OS X, and that it was related to the “IMAP Path Prefix” advanced setting within the Internet Accounts system preference panel. The prefix is set correctly so I was about to give up on this as being an annoying–but–ignorable bug when the very last post in this forum discussion indicated that a cargo-cultish approach of changing the prefix, opening and closing notes, then reverting the setting had fixed it. I can confirm that this solution also worked for me. I kept Mail.app closed for the duration to prevent it being confused, and observed that simply unsetting the value is insufficient, it must temporarily be set to another value, such as “none”, to work.