Hi,
I had similar issue the other day, when I couldn't get Mach out of e-stop. Pin settings/wiring were all OK. I had to rebuild xml file from default one - creating a new profile and copy all the settings from my customized/faulty xml. But I don't think that such errors happen just randomly, I usually get weird Mach behavior after changing pin settings (eg. motor output), and restarting Mach used to fix the problems so far.
Mihael