A couple of things come to mind.
1. a 3 disk raid 5 with no write cache on your system RAID will be slow. You should convert to a mirror.
The MSA20 needs an External RAID controller if I remember correctly. The external RAID controller probably isn't that good if it came with the DL380 G4 and MSA20. It is likely overworked by using a RAID 6 configuration. The best modern controllers struggle with RAID 6. I would consider moving to a RAID 5 with a hot spare or upgrading the RAID controller to a better model with a large cache (256-512) and BBWC.