Danny Parker wrote:
Another difference is that LyX adds

\setcounter{secnumdepth}{3}

\setcounter{tocdepth}{3}

\makeatletter
\makeatother

Any 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

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