What OS version are you running? Any particular reason you didn't download Safari 5.0.6 (Leopard) or 5.1 (Snow Leopard, Lion)?
Good questions...
When I finally got my deuced Mac(hina) back from Apple (*) (Helluva week to have been without it, by the way; I'm still catching up.) I ran Software Update from pre-updated OS X 10.6.8 and, in a radical departure from my usual practice of installing only free-standing d/l's, allowed it to update Safari.
I don't remember which version of Safari SU told me I needed, but it installed v 5.0.5 and, as I discovered after doing some research after reading your post, compounded matters by writing
<dict>
<key>date</key>
<date>2011-07-27T10:40:44Z</date>
<key>displayName</key>
<string>Safari</string>
<key>displayVersion</key>
<string></string>
<key>packageIdentifiers</key>
<array>
<string>com.apple.pkg.Safari51SnowLeopard</string>
</array>
<key>processName</key>
<string>Installer</string>
</dict> (Emphasis added)
to /Library/Receipts/InstallHistory, as a result of which subsequent repeated SU runs left me unaware of v 5.1 until you mentioned it.
After reading your post I d/l'ed the freestanding Safari 5.1 Updater, and both issues I posted are no longer issues.
Thanks for your help
(*) Knowing that they, not I, had my Mac, the "Geniuses" e-mailed, rather than called, me to tell me it was ready for pickup.