I have reverse polarity set for my x and z axis ("$1po=1", "$3po=1"), and always-on power management for all my motors ("$1pm=0", "$2pm=0", "$3pm=0").
If I'm at (0,0,0) in mm mode, send "g0x10y10z10" then "g0x0y0z0", this will start sending current to all motors (3 green lights).
If I send "g0z1" (small positive z move), it makes the move but current stops flowing to motor 3. If I then send "g0z0" (small negative z move), it makes the move and current continues to flow after the move. The same behavior exists for my x axis (current stops flowing after small positive x moves).
I cannot reproduce that behavior on my y axis. If I turn off the reverse polarity ("$1po=0", "$3po=0"), I cannot reproduce the behavior.
In the non-failure case, it seems like there's a small lag between finishing the move, and current flowing continuously, where current does not flow (the light turns off momentarily after finishing a move, then turns back on again).
v6, build 338.12 ($$: http://pastebin.com/EJDGARRf)