Java the language vs. poorly written Java programs.

Straight out, Java is considerably faster than Perl. For maintenance, with similarly skilled developers, Java is better than Perl. Hell, Python is faster than Perl, and significantly easier to maintain as well.

For startup, well, Java isn't meant to be run as a short-run script like Perl. Startup time doesn't matter for anything other than a script that runs in an amount of time similar to startup time, after all. For batch processing, long-running server processes, and other such programs it simply doesn't matter.

Incidentally, if you're talking about Pentaho then yes, it really truly sucks. Don't use it. I'll add, however, that general reporting tools are usually slower than custom-built scripts. The former might not need a programmer involved, however, and the latter definitely does.