I've found the problem!
Some users had been trying to get a new password sent to them by using the new password emailer, but it had not been finding there email addresses, well after pondering the issue and trying to work out why the hell it wasn't working I found that the email address is now stored in my password file as well (gives greater security and privacy). Because the file never contained the email address before, it didnt recognise a valid email address when it saw one (God I am slow sometimes).
What this means is that I have to go back and recreate each persons email address in the password file and then manually chack to make sure it all works! Great eh! Oh well it will be done ASAP