Yep, used to use a maildrop.log before - added one to this server and everything in it is fine.
Have you checked your ispc web panel and made sure it's now using courier in the selection rather then dovecot?
Create a new mailbox and check it's real path - send it an email and see if you get the same problem.
As to using courier-mta, it's most probably quite easily possible, all ispc does is add it's own mysql db stuff for postfix (to lookup users, paths etc), it doesn't actually optimise postfix much at all. Everytime there's an update I have to reconfigure my main.cf - but then I've been using postfix for years so I include a bunch of stuff I gleamed over time. So I don't see the problem making a courier-mta if you are used to it, you just have to have it understand how ispc stores the info in the database everything else is just basic mail server stuff. Even with maildrop you have to add your own quota warnings etc, ispc doesn't do anything like that.
btw, I know you from way back in the old "localnet" days ;-)