After configuring my sites and returning to use FTP I got "Response: 550 .htaccess: Overwrite permission denied" when attempting to overwrite a file. I could delete and then upload the file but this error prevents subversion deployment scripts etc. from working.
I visited http://www.webhostingtalk.com/showthread.php?t=384762 and applied the solution to modules.conf and it worked fine so I have an effective workaround.
I felt you should know that this problem can occur. I'm unsure why the 'global setting' for AllowOverwrite does not work.
I cannot tell exactly what I did to cause it but I updated the FTP directory permissions and reset them to their original values (which required restarting the proftpd service manually btw).