CCEnhancer will always open the x32 CCleaner. On x64 systems; CCleaner x32 will automatically close itself and launch the x64 binary instead.
As for removing the winapp2.ini file; this will only happen if CCEnhancer is in the same directory as CCleaner, and ccleaner.exe is missing or has been renamed.
My guess is that you’ve deleted ccleaner.exe, under the assumption that you don’t need it on an x64 system. If this is correct; you can either reinstall CCleaner, rename CCleaner64.exe or revert back to CCEnhancer 3.1 or older which doesn’t perform the extra checks.