From the QDir doc:
Qt uses "/" as a universal directory separator in the same way that "/" is used as a path separator in URLs. If you always use "/" as a directory separator, Qt will translate your paths to conform to the underlying operating system.
Maybe this applies to qt.conf too? Try
Prefix = c:/Program Files/MyApp
Prefix = c:/Program Files/MyApp
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or
Prefix = "c:/Program Files/MyApp"
Prefix = "c:/Program Files/MyApp"
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