That folder is there to help identify 32-bit programs vs 64-bit programs. It's completely cosmetic, just to help us keep straight which are which because Windows doesn't care. Your problem has absolutely nothing to do with where the program is being installed.
I have windows 7 ultimate 64 bit edition, intel core i5 processor , 8 gb ram,I have installed some programs in c:\program files and some programs in c:\program files(x86) folder.I am getting problems in software's which are installed in c:\program files.whenever i install some software's its automatically installing in c\program files(x86) folder.I installed samsung kies in c:\program files folder and my samsung gt6802 android phone not detecting in my computer.Program icons not showing for the programs which are installed on c:\program files folder.what may be problem.which folder should i choose whether its c:\program files or c:\program files (x86) folder?

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