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