I'm trying to calibrate my Mendel for three days now. I got some great help on Prusa's calculator page. But I still had a problem, Z-axis worked fine when I tested, but when I printed it didn't move (only made some short loud noise). After two days I had the feeling in my guts it is something to do about speed. I upgraded to skeinforge 40 because I found a setting in it to limit the Z-axis speed. It worked like a charm. ;)
Some of the settings still off, I had to set my flow rate on skeinforge to 1700 to get plastic extruded. (I think official setting should be tenth of that). But it may related to the firmware, what I'm using. I may try a different one.