You have to make sure that you .prq file embbed the right operating system conditions in order to be installed correctly on every target machine.
According to this MSDN Page - Windows versions, you'll find what is missing and what lines need to be added.
For example here are only requirements for windows 7 and 8 x86 versions, if you want to deploy on x64 you are missing this kind of xml condition :
-- operatingsystemcondition MajorVersion="6" MinorVersion="0" PlatformId="2" CSDVersion="" Bits="4" ServicePackMajorMin="2"> operatingsystemcondition
Cheers :)