Most drive will not let you do a low level format. What tool did you use?
Can you post OS version (win7, xp, etc), drive model.
How are you measuring write rate? Can you download HDTUNE (google it) and post drive performance and CPU utilization (both are reported by hdtune). If you changed the default block size for the hdtuen benchmark please reset it before running test.
There are a number of things that will do this, example dropping out of DMA into one of the PIO modes.