Not a trick of HJT, but a trick of Windows. Since Hijackthis is a 32-bit program, and windows is 64-bit, Windows will redirect access to certain folders.
trying to access the Program Files folder goes to the Program Files (x86) folder, as I mentioned. so to hijackthis, C:\Program Files\etc... is always inside C:\Program files (x86).
Same for system32 in fact. C:\Windows\System32 redirects to C:\Windows\SysWOW64\, so there are probably registry settings referencing locations in C:\Windows\System32 which HJT cannot access so it assumes they are missing.