The manpages created with yat2m lead to a few warnings. E.g. gpg.1:

$ man --warning -l doc/gpg.1 > /dev/null
<standard input>:153: name expected (got a special character): treated as missing
<standard input>:1449: warning: `GPG_AGENT_INFO'' not defined
<standard input>:1450: warning: `This' not defined
<standard input>:2800: warning: `-'' not defined

The problem is the @samp{} handling, that leads to an apostrophe at the
beginning of the line, which is interpreted as a control character. If you just
want to put it into apostrophes, I would suggest the following handling in yat2m.c:

{ "samp", 0, "\\(aq", "\\(aq" },

So the content is put into apostrophes, but without any linebreaks to work
around leading apostrophes and dots at the beginning of a file, where they are
control characters.

Maybe you further want to surround it with \fB...\fR to make the content bold.