Well, I went to the directory, and the logs start on 12/02, it doesnt seem like any logs before that were saved, but I have had drivepool running for almost six months with no issues. I am uploading those logs, but the issue started before that and I had already forced a measure and a balance. All the folder duplication settings were still correct, I didn't have to make any changes, and once I initiated a remeasure it began duplicating the files in the folders that had lost duplication. Additionally I ran updated scans with Stablebit Scanner, and there are no warnings or issues coming up for any of my physical disks.
I am currently using Drivepool 2.1.1.561. I have no backup services running, I am using Comodo Internet Security pro for AV, however I have it set to request permission before attempting to "fix" anything it flags. Windows 7 Pro.