Hi
I had exactly the same problem. I had to resort to exporting to latex and use plain latex to generate the pdf with correct margins. I also used the IEEEtrans.cls file provided in the conference website, which is much older than the one that comes with miktex (I didn't know how to tell LyX to use the older file, putting it in the same directory as the .lyx file wasn't enough, but it worked for plain latex). Maybe it only has to do with the IEEEtrans class file and not with LyX itself. You might also have some problems with some fonts not being embedded. This causes (at least in my case) the pdf to fail the IEEE PDF eXpress tests. You have to explicitly tell latex (more precisely ps2pdf, which comes with ghostscript) to embed absolutely all fonts. I can give you precise directions if you have this problem as well. Please let me know if any of this was helpful. Regards Neven Boric
