[Koha] Timeout on upgrade script

[Tom Hanstra]

I'm trying to track down a problem that occurs on upgrade.

I have two servers which should be identical because one was cloned from
the other.  However, on the newer, cloned server, when I upgrade from
3.06.04 to the same 3.14.07 version of Koha, the second server times out
with this error in the log:

[Fri Oct 31 14:52:48 2014] [warn] [client 10.41.63.84] Timeout waiting for
output from CGI script /usr/share/koha/intranet/cgi-bin/installer/install.pl,
referer:
https://lupprod-vm.library.nd.edu:8443/cgi-bin/koha/installer/install.pl?step=3
[Fri Oct 31 14:52:48 2014] [error] [client 10.41.63.84] Script timed out
before returning headers: install.pl, referer:
https://lupprod-vm.library.nd.edu:8443/cgi-bin/koha/installer/install.pl?step=3

What might have caused this?  And if I get it, can I be confident that the
upgrade script actually worked despite the timeout or is this indicative of
an error during upgrade?

Thanks,
Tom