A similar issue happened previously but we were able to resolve with a hardware swap keeping the same HD in place. It seems now even though they passed the SMART scans, that it was actually the HD at fault for this matter.
We are not going to deal with this anymore, moving one hard drive to another machine and going to import it into a virtual server like we did with win32 a few days ago.
So working to restore it, to a new hardware/softwware setup now.