Well, no sooner did I say it's all working well in Logic 9.1 (32-bit mode)... I can confirm I get the same error with file names over 30 characters. It works the first time. Once the project is re-opened then indeed Logic cannot find the sample files. You then have to re-load them into the EXS24 editor.
This is not a big deal for me as I don't tend to go over 30 characters for any file names...