You can occasionally get these sort of messages if a full index  gets run, any
chance that happened along with the reboot?

I actually have full updates running weekly on both indexes,
Portal_Content and Non_Portal_Content, on the weekends. So since
then, they've been updated twice each...FYI.

The alerts  show the modified date as being from about two months ago
for some of these files. Any clue why this kind of thing only seems
to be happening with PDFs? Some project team members thought it was
just from opening and closing the files but that can't be it, since
it never occurred before.

Update - I haven't solved this yet, but I've noticed a couple
patterns with this issue:

1) The bulk of these PDF file alerts  have been occurring on
Tuesdays since the time I set up alerts for myself in these document
libraries/areas...that's another thing, I am ruling out the reboot
of the index/job server  causing this to happen, since I never had
alerts set up on these document libraries and areas before the
reboot, otherwise I might have seen old alerts pushed out to me if I
had any assigned to me (this is just an assumption).

2) Most alerts appear about three or four at a time, all for
different documents.

This has been stumping me for a week  and I haven't seen anyone else
in the SPS community with this issue...I'm sure everyone's had times
like these where they feel as if they're unproductive ;) Again, any
help is appreciated, and thanks to Bryan for your response so far.

One more update -

I think I fixed this particular issue  for us...this happens to be a
pretty common bug, and it's apparently caused by v5.0 of the PDF
Ifilter.

I uninstalled v5.0 of the ifilter and then installed v6.0 on Friday,
and so far I haven't received any bogus alerts  yet. I may be
speaking a little soon but I haven't received any false alerts for
nearly a week.

If anyone else has more experience feel free to reply to this post.