Note: 99+% of my usage is on an Atom Pro, so you may need to take this with a grain of salt...
There have been several topics and tutorial on this up on Lynxmotion including:
http://www.lynxmotion.net/viewtopic.php?t=4704It would help to know additional information, such as is your Atom on a board with a serial connector or a USB connector. I assume Serial. Also does your PCs have a normal serial port or are you using a USB to serial adapter? I assume the later. What brand?
With a few adapters I have had, I could tweak the advanced settings like you mentioned and speed it up a lot. With the one I currently using which is a BAFO???, which was suggested by Nathan (AcidTech), I found I was having problems, until I plugged it into an external powered USB 2 Hub. The one I am currently using is from Linksys.
Kurt