The Patch Information tab should indicate the reason for which the patch is considered missing (i.e. file version is less than expected). You can also confirm the detection by identifying the specified file or registry key on the target machine. The file version information for the patch can typically be located within the Microsoft KB article (this number directly correlates to the 'Q' number, and there should be a direct link within the Patch Information tab). It may be the case that the patch is not successfully updating the affected files.
The reason is "file version is less than expected" for all of these updates. What do you feel is the best course of action? To remove .NET Framework 2.0 entirely and re-install the newest version?
We use the original vendor patch during deployment. If the patch is not correctly updating the machine, it may be necessary to work through this with the vendor.
For each individual patch, the actual file being reported as being at a less than expected version is what should be addressed. What is the actual (detected) file version? How does this compare to the published information (i.e. the Microsoft KB article)?
If you would like to post the details regarding any one of the patches with which you are experiencing difficulty (i.e. the Q number of the patch, the operating system of the target machine, and the specifics of the reason for which the detection is indicating that the patch is missing), it would certainly be helpful.
Versions detected vs. version from NetChk Protect as follows:
(32-bit XP Professional OS)
ms11-039 / q2478658 2.0.50727.3053 2.0.50727.5071
ms11-044 / q2518864 2.0.50727.3082 2.0.50727.3623
mswu-385 / q976569 2.0.50727.3082 2.0.50727.3607
ms10-041 / q979909 2.0.50727.3053 2.0.50727.44341
s10-070 / q2418241 2,.50727.3082 2.0.50727.3618
mswu-419 / q982524 2.0.50727.3082 2.0.05727.3053
Although the specific files were not mentioned, the file versions you specified all appear to be consistent with a scan result of a missing patch according to the vendor's published information (excepting "mswu-419 / q982524 2.0.50727.3082 2.0.05727.3053", as it is still unclear as to which file might be being detected at the versions you have specified).
As an example, our detection indicates that Q2478658 is missing on a Windows XP Professional SP3 system due to the System.dll file in the %windir%Microsoft.NETFrameworkv2.0.50727 being at 2.0.50727.3053 (which is a less than expected version). We can also verify that the file detection is correct by viewing the target machine and inspecting the file. Next, we can view the Microsoft KB article found here:
Under the 'File Information' section, we can verify that the file version is indeed less than expected for this patch to be considered installed. After manually installing the patch and power-cycling the machine, if this patch is still not updating the file in question, it may be necessary to turn to the vendor for further support.