Finder doesn't show files that Terminal shows

Running 10.4.4. I have a zip file that expands into a folder containing many subfolders. Finder tells me that the majority of these folders are empty despite the zip file being several MB in size. Opening some, but not all, of the folders forces Finder to tell me what's really there but this doesn't work for all of the folders. I can go into Terminal and see the contents of every folder. What's going on here? This has never happened before. Repairing permissions didn't fix it. It's also happening with other folders not related to the zip file.

Here's an update. The zip file in question contains the latest version of a suite of Java applets that I've been using for some time. The developer just sent me the previous version and the latest version, but the latter was compressed with a different compression tool; he didn't say which one. I moved the two zip files onto my iBook G3 running OS X 10.3.8 and they both unzipped correctly. However, under 10.4.4 only the one compressed with the different compression tool unzipped correctly. This suggests a bug in 10.4.x does it not?

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