Speculation. It's possible that AMD couldn't actually assist Microsoft in making low level modifications to the Windows kernel/scheduler without AMD first entering into a formal partnership to work on that aspect of the Windows kernel. As far as I know, without some type of formal partnership to share information/ip, the depth of the partnership is just the hardware vendor sending engineering samples and answering questions without actually looking at the low level code. No idea because this type of information never seems to be made public by companies where closed source closely guarded software is their bread and butter.
Remember that Windows is closed source proprietary software. As a result maybe Microsoft probably wouldn't confirm if there was an issue, the exact nature, etc, unless AMD entered into a formal partnership and kept failing to solve the issue on their own. Why? Because in Microsoft's eyes it would be disclosing proprietary information about the nature of the Windows kernel and scheduler.
Anyway this is just speculation but considering that the Linux, FreeBSD, and XNUmacOS kernels (all open source) had these problems solved a long time ago, I suspect it might be close to the truth.