use base qw(xxx); is equivalent to require xxx; our @ISA=qw(xxx);.
Although you would be somewhat challanged to discover this from the documentation this isn't entirely true. It isn't exactly equivalent since base explicitly ignores errors from require that indicate the module cannot be loaded. This is handy since it allows you to write things like this:
# ... some methods ...
use base qw(Foo);
where no modules are involved at all. Take a look at the source for details.
As Aristotle points out the lack of an import isn't the cause of the problem. Class::Factory works perfectly well with use base (at least on my box :-)