I do not think you are doing anything wrong. Most programmes install in the 32 bit version in C:\Programme files(x86). Fro example in Photoshop CS5, it installs both versions , and I use both since for scanning using the TWAIN interface there is no 64 bit support, but on the other hand the TWAIN interferes with the file/automate/batch command. Just go with the flow, use the 64 bit option if it is offered.
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