Since Vista M$ is doing strange and mostly customer uncomfortable things in system directories ... shall help for security ...  But hidding files, prohibiting writing to files and such more is mostly a problem to application and normal user is blocked out. Ok, you can change a lot of system settings to avoid this but you need in deepth knowledge M$'s curious minds ...

Therefor my best advice to avoid such trouble: Don't use Program Files directories if not essential needed (normally no program is such extrem). Instead create a own directory parallel to Program Files, e.g. MySoftware or such and install all your program into that. M$ is not aware of users creating their own locations and therefor they will leave those directories alone ... no nasty silly thinghs happening and you should find all your stuff ... :-)