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Our scan detection logic looks at the file and registry level to determine the existence (or absence) of a patch. Our default 'Security Patch Scan' will attempt to detect all supported products installed on a target machine, and will then scan for 'Security Patches'. We define 'Security Patches' as any patch which addresses a known vulnerability. If a patch does not specifically address a vulnerability, it will be classified as either a 'Non-Security Patch', or a 'Security Tool'. Our default 'WUScan' will scan for both 'Security Patches' and 'Non-Security Patches'. In order to include scanning for 'Security Tools', you will need to create a custom patch scan template.
We have a scan template that I attempted to use with the following settings: Product Filter->Scan All, Patch Filter->Scan All, Patch Type Filter->Scan All. On the general Tab we have both missing and installed patched selected with include effectively installed patches also selected. This still does not find the quicktime, real player and missing java updates. Granted some of these missing updates found by qualys are old, but I don't understand why it is not finding the newer ones.
Are any patches being detected as missing or installed? If you can provide an example of a patch which you are expecting to see detected as missing (e.g. the Bulletin ID would be very helpful), we can take a closer look. It may also be the case that the patch was superceded by a later patch. Is the patch detected as installed (or effectively installed)?
I can give you a very broad example that is strange. We have some computers that are showing having Quicktime 6.2 installed. When I run full scans with all settings selected it is finding no quicktime updates at all. Same thing for Real Player.
We currently only scan for QuickTime versions 7.0.4 and higher. So if you had Quicktime 7.0.4 or higher on any of your machines, it would show the latest version as missing.