Publish online not working.

I'd created an alternate layout in a 22-page illustration-heavy document. Then I deleted the original layout. Everything looks fine in ID and the file exports perfectly to a PDF, but now it won't publish online. It goes through all the motions and looks quite successful, but when I view the doc most of the graphics are missing and weirdly, the page numbers only show the letter of the master page (they do not update to show the page numbers). But like I said, if I export to a PDF everything works perfectly.

Anyone have any idea what's going on? Have tried re-starting ID and also saving the file under another name. Same results.

Thanks!

Hal