Do you have a drive thats on the approved hardware list? I had a 2 drives that poped out on my 509 (using all bays).....they were not on the list. After replacing them with checked drives it worked like a char. I do have a Q35 connected via eSATA that popped out every now and than, it checked out that the drive was not on the list to and after switching to a compatible drive it worked there to. Try it if you have the oppurtunity.
-TS-459 Pro+ 3.8.1 , RAID 5 running 10 domains with about 50k hits/month
-Services: web,mysql,ftp,ssl,filemanager, RTRR
-Remote Replicating to second site to a TS-659+, 3.8.1, RAID5
-PhpMyAdmin 3.5.3, TinyWebGallery 1.8.8, AjaXplorer 4.2.3, Wordpress 3.5
-Using it for my blog (http://blog.lentzit.com