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Check which version of Safari is actually loaded. I recently reinstalled the 10.6.8 Combo Update v1.1 and discovered that Safari was still at version 5.0.5, rather than 5.1.7, the latest release. Software Update did NOT discover that there was an update available, and did not offer to install it.
Searching Apple quickly located the WINDOWS version of Safari 5.1.7, but no link to the OS X 10.6.8 version.
OS X Safari 5.1.7 is available at this link from this non-Apple source at macupdate.com, a reliable vendor of Mac software. Click on 'Download Older Release' to get the correct one for 10.6.8.
I also use the Click-to-Flash Extension to eliminate automatically loading most Flash content. You can 'whitelist' websites where you want to load and display Flash content automatically, and also set the preference to display HTML5 content when available.