I hope this is in the right place. So this has happened to me a couple times .
First with server 2008 R2 and exchange 2010. My servers replicate offsite using zerto and I was testing failover and noticed the drive D was offline. Brought it online then rebooted and everything was fine.
So I just build a server 2012 R2 Datacenter edition VM on my production servers, gave it a second disk, initialized it, formatted it and assigned it the drive letter D. Rebooted after installing 3 windows updates and the "Disk 1" (drive D) was offline. There is nothing on this server at all. It's a fresh install.
I'm running ESXi 5.5 build 2302651 with hardware version 8 and VMware tools version 9.4.11 build 2400950. The SCSI controller type is Paravirtual for all my VM's. My DR site where I tested my failover is DAS and my production site is iscsi. So I don't think the underlying storage type matters.
From my experience when you see this kind of stuff happen in multiple situations it will happen again. My worry is what if one of my hosts decides to die and HA kicks in and the disk is offline when it boots.
It looks like others are having this same trouble. I also posted in that thread.
I am experiencing the same issue with ESXi 5.5, Server 2012 R2 VMs, hardware version 8, and additional drives booting offline that are connected on different LSI Logic SAS controllers. Please let me know if you find a resolution to this issue.