Hey Mjohnson,
when you rewrote the lines, did you repair a custom template or did you just correct the php.ini file directly?
If you make changes to the php.ini directly, your changes *will not* survive an upgrade/update-event.
If on the other hand, you found a custom template and made the repairs to it, all *should* be fine.
No, this doesn't help figure out why the template got messed up in the first place.
1) Did you recently add any new rpm's or apps?
2) Are you the only admin on this machine?
3) Were you seeing any odd behavior before the update?
If you suspect there is a bug here, try to document what lead up to the problem: log files, added rpms, new apps etc.
Then post a bug in Bugzilla(or bugtracker).
Good luck
Joe
Side Note: it may be worth the risk to try doing a "/sbin/e-smith/signal-event post-upgrade"
then,
"/sbin/e-smith/signal-event reboot".
If the php.ini file stays working everything should be fine.
Might be better off finding out now if the problem is going to persist.