Can you describe your setup in more depth?
I followed the perfect server setup for Debian Lenny and ISPConfig3 here on HowtoForge. In that tutorial, Squirrelmail is installed.
I have offered both Squirrelmail and Roundcube options to my users on my previous system that I configued manually (i.e. does not use ISPConfig). Feedback from users are mixed. Many prefer to use Roundcube, but the biggest drawback has been the ability to change their own passwords and autoresponders. Those features are offered in the Squirrelmail configuation I use.
I see these plugins as my ability to address some of the negative feedback I have received about Roundcube lack of features.
Did you just create a site to house Roundcube within ISPConfig and then upload the files there? Then you upload and overwrite the files as described in the text file within that directory?