Problems with latest security update

Hi there,
After I've installed latest security update via Software Update in MAC OS X some problems emerged.
First and mos visible thing .html and .htm documents on my desktop does not have safari icon anymore, they have some blank icon and doubleclick on them does not start-up Safari, why?
Second, how can I found out what else was(is) changed or modified in my system?
Third, as first aid I've run daily, weekly and monthly maintenance scripts as well as permissions repair (2x).
Does not help! I know, that running daily, weekly and
monthly and perm repair is like opening window because water tap is leaking but that was first thing I did...
iBook G4 Mac OS X (10.4.5) 1.33 GHz, 512 MB, 12-inch

I've tryed to repair permissions at least 3x, and also run update_prebindings
Problem prevails, even if I log in as other/new user, indicating that issue is system-wide not user wide.
http://www.jirkacech.com/files/Tiger-problemy-screeshot.png
note 'empty' icon at newly saved webarchive, as well as fact that Safari is now 2x in dock, once I newly add it (with correct icon) second time original with silly icon with document and triangles....
I am getting desperate.
iBook, 1,33 GHz Mac OS X (10.4.3)

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