Danny Parker wrote:
Another difference is that LyX adds\setcounter{secnumdepth}{3} \setcounter{tocdepth}{3} \makeatletter \makeatotherAny idea why LyX is adding these files?
Yes, to control the TOC. But they are harmless.The crucial difference is that \maketitle comes earlier---probably too early---in the LyX file. Can you post the LyX file? And the phm.style file? I can't compile anything without that.
Is there a way in LyX to edit the LaTex Source directly?
No. rh