Loud beep when updating to 10.8.1?

Hi,
About half way of updating to 10.8.1 on my iMac it made about a 3/4 second BEEP

Not sure, but have you tried downloading the standalone updater from the Apple Support site, rather than doing it via the Software Update menu?
http://support.apple.com/kb/DL1571
As regards slow boot, sometimes re-selecting the startup disk helps:
System Preferences>Startup Disk, select Macintosh HD, Mac OS X 10.8.x and click on restart.

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