I'm on Logos Bible Software 4.2a Beta 7 (4.21.5.0402) and first noticed this issue yesterday while adding some new resources to my library. For some reason the book covers on my Mac installation didn't show up for those books, but they did show up correctly on my Windows 7 Logos installation.
So I played with it for a while and deleted the catalog.db file in the LibraryCatalog folder numerous times to force it to rebuild the database, but all to no avail. Logos would rebuild that file, but it would only be about a fifth of the size of the original file and instead of a few covers missing, the majority would be missing.
So last night I just deleted my entire Logos installation and installed everything from scratch. Redownloaded the resources and everything. This morning when checking it I found the catalog.db file back to its normal size, but still with a number of resources missing their cover images. So even with a reinstall, the problem remains.
I've included a screen grab of the problem just to show what it looks like: 
Also included here are my log files, which seem to hint at the problem: 4572.Log Files.zip
02/19/2011 16:24:29 | WARN | 6 | LibraryCatalog | No metadata found for resource '{782DBF4D-222B-4D8D-939B-77611925A144}'.
This warning comes up about 30 times or so, which seems about right for the number of resources missing a cover.
Any way to fix this problem?