I need to be sure which schematic you followed to do your conversion.
For the "version 2" schematic that is at
http://www.cnczone.com/forums/attach...4&d=1283013610 (and which is referenced in post #1 of the thread at
http://www.cnczone.com/forums/genera...y_chinese.html), my analysis of the circuit indicates that Step Low Active should be Green in order to get a negative-going step pulse on the TB6560's step (clk) pin.
The unmodified board should work with Step Low Active set to Red.
The modification thread is a long one, though, and so it's possible that there are other schematics showing recommended fixes that I may have missed - so, can you point me toward exactly which schematic you used?