For anyone interested, we managed to get it going by adding into pre_virtualhost_global.conf, for each VirtualHost

    PerlOptions +Parent
    PerlSwitches -Mlib=/home/domain.com/lib/perl
[download]

According to the Cpanel tech guys, this means that it will run a perl instance separately per domain (which is what we need)

We've got it setup on 2 sites now, and as far as I can see its working a charm (no inter-sharing files at all - which is great!