How interesting - if it was systemic it would be a problem with all the drives. It is just these 2 drives that dismount? And they have dismounted even when they are installed in a different bay, a drive bay where you don't ever see a problem?
First, make sure the eSATA card is in slot 3 or 4 - not slot 2.
Open Apple System Profiler, go to Extensions under Software and make certain that the driver for the card is correct. It should read SiliconImage3124u.kext version 2.1.4
It may be worth the effort to take those two drives out of their trays and install in the internal MacPro trays. Worth it to see if the issue is the drives themselves.
Thanks for posting. We'll figure it out.
"I am a mortal enemy to arbitrary government and unlimited power. I am naturally very jealous for the rights and liberties of my country, and the least encroachment of those invaluable privileges is apt to make my blood boil."