This here is the most important post in the thread.
If you are using SV35 drives, then you will run into issues.
The difference between desktop-class and enterprise-class disks are mostly down to error handling. In a desktop-class drive, the disk will continue to attempt to recover data from a bad sector over and over. This increases data access latency, and the drive locks up during the request. Almost all RAID array controllers, software or hardware, will see this as a disk failure, and fail the disk instead.
Enterprise-class disks have error-handling that's internal and specific to the disk, and work with RAID controllers. They will mark a sector as bad instead of retrying, allocate a spare sector to it's place, and request that the RAID array rebuild the block the sector was part of. This recovers the data and allows the read/write operation to complete in a matter of hundreds of milliseconds. This behaviour is optimal.
Check your drives and make sure you are using enterprise-class hardware in your RAID array.
As other's have said, SuperMicro is a huge OEM vendor for many other companies. Your RAID controller is probably a stock-standard LSI, Adaptec, or similar... or you may even be running Windows Server Storage Edition, and utilizing software RAID. These days, software RAID is as good as hardware RAID in dedicated appliances.
There is no reason to change the server... but there are MANY reasons to change the hard disks.
I personally recommend the Western Digital AV-GP series. These are enterprise-class 24/7 drives running 7200 RPM and are meant for surveillance applications. They are RAID compatible.