We are moving to CF11 and setup 2 websites exactly and both website provide exactly same components - but one is giving error - 500 - 64 bit/34 bit issue

I think the WSCONFIG folder for other site is 2 and I created VD jakarta to point to 2. for the site I am seeing issue - it is pointing to 1 and seeing some restriction file.
I tried to create multiple times new site so it creates and point to new folder in wsconfig, but everytime it is pointing to 1.
is there anyway I can manually update ?
This site has .NET componenets, if I enable 32 bit - my CFM pages give above error, IF I don;t enable .NET is giving an error.
but, this issue is not there on the other site on same VM.
