Hi Derobert,
Overtime, as the RAID array fills with data, it will slow down but I wouldn't expect it to drop off by as much as nearly 50%. My first guess would be that it is due to the F6 BIOS and it might be worth going back to the F5 to see if that improves things again.
Also check your RAID settings haven't been altered when you flashed the BIOS, they shouldn't have done so but double check to make sure, especially with the stripe size that you are using as this may have defaulted to a lower setting.