I had exactly the same problem as this and found that it was caused by some kind of installation adding an extra line to my iis applicationHosts.config file.
The offending line was in the file C:\Windows\System32\inetsrv\config\applicationHost.config. The "isapiFilters" section should look like:
EDIT: Gah, the XML's close enough.
<isapiFilters>
<clear />
<filter name="ASP.Net_2.0.50727.0" path="%windir%\Microsoft.NET\Framework\v2.0.50727\aspnet_filter.dll" enabled="true" enableCache="true" preCondition="bitness32" />
<filter name="ASP.Net_2.0.50727-64" path="%windir%\Microsoft.NET\Framework64\v2.0.50727\aspnet_filter.dll" enabled="true" enableCache="true" preCondition="bitness64" />
</isapiFilters>
My problem was that an extra line had been added before the first two, directly referencing the aspnet_filter.dll with a fixed path, the double-backslash you see in the error, but crucially without the "bitness" precondition, meaning that both 32 and 64 bit components were being run against the 32 bit aspnet_filter.dll.
I deleted the offending line, and all has started working again.
You may find that the command you tried above has changed one of your application pools to 32 bit from 64 bit. You may need to change it back if it wasn't actually the problem.