+1. Same problem here
Notecaddy has just been updated to v.2.9.9009. Please try the new version to see if this issue is fixed.
Also, please move the Notecaddy folder to your desktop to act as backup, its located here: C:\Users\YourUsername\AppData\Roaming\Max Value Software\Holdem Manager\3.0\AppsData. After this restart HM3. Allow it time to download and install Notecaddy. Reimport definitions and recreate notes for your database.
If it still happens after these steps, please open a ticket with the send feedback option in HM3 with the logs for us to have a look at them. Also include any info that might help us. Pokerooms you are playing on, kind of game (cash/MTT), HUD imported from HM2 to HM3 or HM3 HUD, definitions imported from HM2 or created in HM3?
All of this will help getting to the root of this and fixing ASAP.