There are a few things that need to be considered here, I'm afraid:
- First, of course, changing the Write Mode for the logical drive should not show any effect for a READ test. If it did, I'd be very astonished (OK, in the past there existed controllers that increased the size of their read cache when the write cache size got decreased, but that's a different story...)
- Then, the faulty BBU would only affect write operations, as read operations would still benefit from the still operable cache. Or should I write: They would, if you hadn't disabled EVERYTHING that could have positive effect.
You might want to have a look at Fujitsu's White Paper
on RAID controller performance. They're discussing RAID5 instead of RAID6, but, well, Christmas is still a few days away...
If you wish to optimize your system for your test (and not for its initial purpose of acting as a server system), then I'd suggest you should enable read-ahead, and perhaps the disks' cache as well.
The initially mentioned "unexpected sense" for disk (3) is an error that occurred during a read operation as well. It was recovered, but did this error show up only once, or do you get messages like this quite often, especially when your test runs?
If your system is still under warranty, you might want to get in contact with Fujitsu's support team, in order to get the RAID Manager logs checked. There may be a disk getting weak or two.
You did install latest versions of BIOS, firmware, driver for the RAID controller, or didn't you?
As you already noticed, it's not a good idea to perform a lengthy time-consuming test on a Windows server system over night. These systems tend to spend their "free" time optimizing themselves, and I'd bet that during the period with the red "slow" boxes, this server was performing database reorganisation or backup or whatever else...
If you wish to get correct values (well,sort of...), you need to remove any possible OS (or application) duty from the disk (or disks) being checked during the test runtime, besides the test application's duties, of course.