Well, I found Don's comment intriguiging, so I gave it a try on some Oracle backed ACSes. I was unable to find a problem installing packages with ACS classic 4.2, but I had a heap of trouble installing with a checked-out version of ACS somewhere around 4.1.
So I'd begin by checking what ACS version you're on and upgrading if not on 4.2 (upgrading was *surprisingly* painless, by the way - it looks like APM is finally smart enough to handle the upgrade. I untarred, moved my custom packages over to my new directory, pointed my server's .ini file to the new directory and kicked it, went to /acs-admin/apm/, and clicked on "Install packages", and *poof* it upgraded everything. Ran into one annoying Oracle "existing state of package has been discarded" message, but I don't think that's the ACS' fault, I think that's Oracle being annoying. Your mileage may vary, of course; I haven't been able to track down any documentation about whether that is really how you're supposed to upgrade a 4.X server.)