The log you've sent here shows that one of your partitions on a Physical drive #2 is marked as both HIDDEN and ACTIVE which is a serious red flag for anti-rootkit engine. That's why it throws the detection. But this is not all: the file system for this partition could not be determined for some reason so anti-rootkit engine considers this as a malicious partition and completely removes that. I spent a day experimenting with the latest version of the BootIt NG Bare Metal trying different options and I was unable to achieve such results when the partition was marked both HIDDEN and ACTIVE at the