According to Microsoft, "Most programs designed for the 32-bit version of Windows will work on the 64-bit version of Windows. Notable exceptions are many antivirus programs. Device drivers designed for the 32-bit version of Windows don't work on computers running a 64-bit version of Windows. If you're trying to install a printer or other device that only has 32-bit drivers available, it won't work correctly on a 64-bit version of Windows." 32-bit and 64-bit Windows: frequently asked questions
I also went to the Microsoft Compatibility Center and it too says that MySQL Tools (Version 5) should be compatible with 64-bit Windows 7. Windows Compatibility Center: Find Updates, Drivers, & Downloads for Windows 8, Windows RT and Windows 7
However ... (you knew there was going to be a "however", didn't you?
) Depending on how old your Apache/MySQL/PHP is it may not be fully 64-bit compatible. You could try running it in Compatibility Mode to see if that makes a difference. Compatibility Mode