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Hi Eoin,
I'm the head of the development team of CP Pro on SBSH.net Mobile Software and our software also must be installed on the default directory and we have several files stored in the \Windows folder so I'll try to answer your question.
I'll answer from our product "Calendar Plus Professional" point of view, which is a today screen plug-in and behaves a bit different from a regular stand-alone program, but the same answer is right for any "large" software that connects to the main PIM database and etc.
The way Microsoft designed the OS, many of the databases and important DLL's are located on the \Windows folder and software that want to connect to the default PIM databases need to sit under the same folder, the same thing for any Today screen plug-in that must be installed in the \Windows folder.
I think it might also work if it will be installed in a different folder but this is not documented so we never tried it (you don't want to try things that are not documented because you can't really know if they will work on all devices etc.).
One thing is for sure, if a program is designed to work on the default install dir only, trying to move it's files will cause it not to work any more almost all the time, this is because that at the time of the installation the software writes values in the registry that specify other software-depended files location, moving these files will cause the software not to work any more.
I hope it helped...
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