Not to get to deep into the weeds, here's the gist.
A SysAdmin of ours created GPOs on the Domain Controllers Policy (DCP) and we've been having time issues ever since.
Neither he nor I know if the Windows Time Service was configure via GPO previously or not.
I configured the PDC Emulator via command line and got everything working fine.
However, the GPOs for Windows Time Service is still active. I'm asking just for clarification, but I'm pretty sure I know the answer.
Should I re-configure the DCP: Windows Time Service GPOs to "NOT CONFIGURED"?
Also, on the backup Domain Controller (non-PDC), if I configure it for "syncfromflags:domhier" how do I get this system to act as a backup time server for my Linux (SUSE 11) machines which are pointing to the PDC and working properly, but they are not able to get time from the backup DC aka non-PDC emulator? (this is my real question for this thread).
Yes.
Here's the technet reference. Note that it doesn't say anything about setting up GPOs to change the NTP client behaviour on DCs (because that would be kind of dumb without other good reasons).
(source: technet)
Refer to this SF question I guess: Sync Linux to Windows 2003/2008 Natively