For the MSR partiation, this depends if the drive is MBR or GPT, and sometimes, how it was initialized+partitioned. Either way, the presence/lack shouldn't effect things. My pool has a mix of these, and has for a long while.
As for the non-GPT drive, it's possible that there was some partitioning error? Eg, if the system was unstable and rebooting/BSODing, any time that the disk is being written to, there is a chance of corruption/damage.
You can use diskpart or powershell to fix this. IIRC. But it shouldn't be too big of an issue. And if you're using Windows Server, the Multipath I/O feature can "fix" this.
Also, I would recommend checking the event viewer for disk, file system and controller errors. They may point to a specific disk.
But Also, if you haven't, run a CHKDSK pass on *all* of the disks (except to pool)