I noticed an odd message on my Rostock Max v2 when using S3D, "Steppers Disabled" at some point while it's printing (but everything is still running). Not sure if it's related but I noticed if Windows turns off my monitor (sleep is disabled) the printer will pause, make a click, then continue. Once it lost track of where it was. I've since disable the monitor turning off.
I don't recall anything like this before the current update, but I haven't been using S3D for very long.
Computer is running Windows 7, 64 bit.
Re: Steppers Disabled
That is a firmware message, so it is coming from the bot, not from the software. My guess would by that your inactivity timeouts are set too low to where one of the axes are timing out during the print. This "feature" would disable the current to the motor if it wasn't used for a specified duration of time to help save electricity.