This was initially a request for help, until I managed to solve it while typing out this message :-) Now, maybe it'll be able to help someone else.

Some of our users want to be able to access the IMAP data via other clients, such as squirrelmail (don't ask :-)

That seems simple enough, and worked fine until we actually tried accessing an account with mail in it. Now that we've migrated mail to this account, we're receiving the following error when attempting to view the Inbox in squirrelmail:

ERROR : Bad or malformed request.
Query: SORT (ARRIVAL) ISO-8859-1 ALL
Server responded: parse error: command not implemented
I had also received "parse error: command not permitted with UID" at one point.

The problem is the sort... which doesn't seem to currently be supported by Zimbra.

Squirrelmail offers a number of config options that can be altered in it's config.php (on RedHat/CentOS systems, this is in /etc/squirrelmail/config.php).

In there, is an option named "allow_server_sort", which by default, is "true".

Simply change it to "false" to get things working.

Have fun :-)