Sounds like you have your Notes set to sync with a non-iCloud email account. When you sync notes with Yahoo, Google, or Hotmail (not sure about that one) they actually sync with a special Notes folder in your email.
If you edit or modify those notes in email, in any way, the syncing is broken. While I've never heard of it happening, I suppose something going on with your email account might break it as well.
If you do have an iCloud account I suggest you go through each of your mail accounts in Settings > Mail, Contacts, Calendars > Accounts and turn off Email syncing; except for iCloud.
Then go to Settings > Notes and make sure iCloud is your default account.
You'll probably want to copy all your notes somewhere else first; though you should get the option to keep notes locally when you turn off an account.
If it does end up creating a local note folder, there is a way to combine that back with iCloud later, if you decide you want to.
The other thing you can do, and what I do, is use a different note taking app as your primary notes app. I'm fond of Evernote; though to get the full benefit of their service on iOS you need a Prime account at about $5 a month.
But, if your note taking is moderate, and you're willing to settle for internet only access of your notes on the iPad, the free service is plenty.
Of course, there is no shortage of other fine note taking apps.
