Which theme was it..?

It's true that themes with a BootX file will not work with new computer with 10.2.4 preinstalled, because the have a newer BootX file. However, it's safe to apply themes if you upgraded an older computer to 10.2.4.

I will update my themes during the next week so that none of them install the BootX file, because I'm guessing that Apple will eventually upgrade it for everyone and then it will cause a lot of problems.