OK, this may or may not be of interest to the developers so please take it with a grain of salt. The value appears to be persisting to the xml file. Howeve, if you enter the motor tuning and exit, it decrements it. To ensure this was happening, I did the following:
1. Enter Motor Tuning, set the step pulse to 4 and the dir pulse to 4, save and exit Mach3. Checked the xml file and settings were 4980 and 4980 respectively.
2. Enter Motor Tuning, change nothing but press Save and then exit Mach 3. Checked the xml file and the settings were 3984 and 3984 respectively.
3. Enter Motor Tuning, change nothing but press Save and then exit Mach 3. Checked the xml file and the settings were 2988 and 2988 respectively.
4. Enter Motor Tuning, change nothing but press Save and then exit Mach 3. Checked the xml file and the settings were 1992 and 1992 respectively.
5. Enter Motor Tuning, change nothing but press Save and then exit Mach 3. Checked the xml file and the settings were 996 and 996 respectively.
This appears to be a programmatic bug when saving the settings. For some reason it's decrementing each time. Hope this helps. Good news is were not crazy.
Best Regards.
Carl