The error indicates that IIS is in 32 bit mode, while this application is a 64 b it application and thus not compatible.
I
was trying to install a new WSS v3 Sharepoint on a 64 bit Windows 2003 server
today but the installation was giving some error saying i would need to allow
ASP.NET 2.0 in the web server extension in IIS. 
Looking
at the IIS there was a ASP.NET 2.0 32 bit allowed but not for a 64 bit.
I
tried registering the aspnet_regiis but no luck by doing so:
For the 32 bit verison
%SYSTEMROOT%\Microsoft.NET\Framework\v2.0.50727\aspnet_regiis.exe -i
For the 64bit version
%SYSTEMROOT%\Microsoft.NET\Framework64\v2.0.50727\aspnet_regiis.exe
-i
I get the error "The error indicates that IIS is in 32 bit mode, while this application is a 64 b it application and thus not compatible."
The
difference is the \Framework64 folders
So my next guess was to find a way to disable the 32 bit and
then allow the 64 bit version.
And luckily enough i found this link
MS to the rescue
So just ran : cscript %SYSTEMDRIVE%\inetpub\adminscripts\adsutil.vbs SET W3SVC/AppPools/Enable32bitAppOnWin64 0
and the registered the
%SYSTEMROOT%\Microsoft.NET\Framework64\v2.0.50727\aspnet_regiis.exe
-i
and that was it 
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