Like IO operations from 32-bit applications on System32 are redirected to SysWOW64, 32-bit programs accessing certain parts of the Registry are redirected to a different location. For example, operations on HKLM\Software will go to the equivalent path under HKLM\Software\WOW6432Node. There are some exceptions, where structures are shared between the two Registry views. MSDN has a list of affected locations.
If a Registry change in the normal parts only seems to affect some applications, you probably need to make it in the 32-bit section as well.
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