It's more of a security issue with programs such as HS and GG. As the methods they use to hide and protect games are also used in malware. However, windows also is aware of it's use as malware and is thus making it harder for malware to operate on the OS, as well as making it harder for game protection systems to protect games.
It's like installing to Anti-viruses on one PC. They'll attack each other. Same with a protection system. It's pretty much, indirect and uncontrollably MS Windows 7 VS GG. Both are trying to protect something. Because windows has far more control over the computer itself, it will always win. GG and HS need to find a way to take back control without being considered malware or doing dangerous things to one's PC.