I am doing the same with a boss5. I had to go in HyperTerminal, properties and set a 1 to 2 mill sec. pause between lines and characters. I was transferring the first line ok then the dam?
Also there is the baud rate thing but if you are getting the "BOSS X INPUT or BOSS X EDIT you must be close or right on. As Stephen stated make sure you have the caps locked. When I hit edit and get the BOSS prompt I hit "I" enter, this puts the mill in input mode. You should be able to see each line of code echoed back to the PC as the mill receives it. Then "L" enter to list it back. You can also edit the code stored in the mill from the PC it’s not very fun. Controle "Z" then run the mill.
Since mi mill is a BOSS 5 things may differ.
Hope this helps.
Stephen