There’s a new update to InDesign CS4. Version 6.0.2. The update fixes lots of other stuff, so you may want to look at the release notes to see what’s fixed that is not related to the EPUB export, I’m only going to talk about the EPUB plug-in.
Issues fixed by the update are:
Content is dropped during export to Digital Editions when two or more documents are included in a book. *
This was an issue where, if you have more than one document in a book file, and you export an EPUB from the book file, the first document is the only one that’s guaranteed to have any content.
Export for Digital Editions will put underscores, rather than spaces, in the Contents if TOCStyle is not used. *
This is the case where you use the InDesign Book feature to export a set of documents, and the file names end up in the “Contents” panel in ADE. The problem was that if you had spaces in the filenames, the export filter would replace them with underscores. You’ll now get spaces rather than having them replaced by underscores.
The issues that were fixed in previous updates, in case you missed them:
Bold (and in some cases italic) won’t work when exporting an InDesign document to Digital Editions. 
It was actually that bold wasn’t working when it wasn’t in the paragraph style, and italic worked only if you did not embed the font. Both were fixed in the 6.0.1 update, but are also fixed in the 6.0.2 update.
Exporting to Digital Editions fails with an error in the Italian and French version. 
The dialog wasn’t working, which had prevented the plug-in from being used.So with this update you should be getting much better output from InDesign CS4.