Are all of the resources (fonts, SVG files, etc.) properly declared in the OPF file? IIRC, iBooks ignores any files that aren't explicitly listed in the manifest even if they are referenced by other files.
Edit: Also found this thread:
I filed a bug with Apple. If they bounce it back to me and point out a flaw in the content, I'll let you both know. Otherwise, hopefully they'll fix it at some point.
If you're just using SVG to make the cover look good when you view the cover page, you can probably work around the problem by setting the cover image to the actual PNG file that you're using for the underlying image data. Of course, if your actual SVG is more complicated (adding text on top of that or whatever), then that obviously won't work.