The proprietary software is unaffected by the GPL so long common sense (ie in layman terms) tells you that they are a separate program with the GNU/Linux parts.
The problems comes when people want to stretch the definition of separate programs. In those cases, contacting lawyers and seeking out the authors intent seems to be the only viable option (for example, the case with Linux modules).
That was what I thought was the case, but wasn't 100%.
I worked for some folks who were making an ubuntu based network-monitoring appliance a couple of years ago, one day they freaked out about the GPL and decided (absent any legal advice) to make us port the project to NetBSD. They refused to consult a lawyer because it would be too expensive apparently, but would have been far cheaper than all the developer time... I suppose at least I got to add NetBSD porting to my cv :)
The problems comes when people want to stretch the definition of separate programs. In those cases, contacting lawyers and seeking out the authors intent seems to be the only viable option (for example, the case with Linux modules).