Just want to be reply 428 and say I have the same problem..
I run OS 10.9.2
Macbook pro (late 2011)
Pegasus R4 Thunderbolt raid, Cinema LED display daisy chained through Pegasus.
Old cinema HD display conected throug display link (USB)
And 2 WD drives daisychained through Firewire 800 port.
When the computer goes to sleep, it ejects only the pegasus (not the firewire drives) and gives me the inciorrect ejected drive warning when I wake it up. I have to powercycle the pegasus to get it to remount.
Sometimes I also find in the morning the the comuter has restarted itself.
No options in ebergy saver make a difference and Jettison works in that it ejects the drives (and removes the incorrect eject warning), but it does not re-mount the Pegasus when I wake up the computer, I still need to power cycle. (It does re-mount the firewire drives)
I had this problem before, but then went away (I assumed with the last software update) But I just got my logic board replaced and the problem is back.
I really hope we will get a fix in the next software update..
Danielle