I'm having trouble reproducing this situation, so I kindly ask all the upvoters to provide additional information:
1) Does the "busy" tooltip stay even after 1 minute of CN being idle?
2) OS version, CN version, Dropbox version?
3) How often this happens?
4) Does CN run all the time in background on all PCs?
5) Does restarting CN help?
6) (Advanced) Does Process Explorer show cintanotes.db locked by cintanotes.exe? (see here how to check: http://cintanotes.com/forum/viewtopic.php?f=6&t=607&p=2999)

Thanks!

Thanks for the ideas! Option 3 makes most sense to me, this is how I envisioned it actually.

I like your draft. The obious solution to the title question would be
to leave the title unprotected. This should pose no serious problem.
Another solution would be to hide the protected notes completely until you pick this tag,
but it is less consistent.

Thanks for the info! The settings file should be in C:\Users\%UserName%\AppData\Local\VirtualStore\Program Files\CintaNotes\. Please send it to jenter@cintanotes.com

You don't need to arrange again, just when export switch view to manual, as you'd like to see it after import.

Proposed fix: http://cintanotes.com/forum/download/file.php?id=95