Greg says it is a Mach issue:
I don't have any control over the dwell commands since Mach interprets the gcode and then commands the plugin. I brought this up to Brian and he was going to look into it. The SmoothStepper can do very accurate dwells if Mach commands it properly. I would ask Brian and see if he can change Mach. Dwells can be implemented as zero-velocity moves, and the plugin doesn't need to do anything. Or he could send a notification and the plugin can send a command to the device to have it delay.
In any case, megabytes of code and macros can be changed from ms to seconds in about an hour, assuming one is DOS-savvy, and with judicious use of grep. Here's what I did:
1) There are four cases to search for: "G04 P", "G04P", "G4 P", and "G4P". Both your macros folder (and subfolders) and your NC folders (and subfolders) must be searched.
2) Search each with: grep -irl "G04 P" *.* >go.bat This puts each filename with the occurrence into a list in a batch file. (the grep options are "i"=case insensitive, "r"=recurse dir tree, "l" = output only filenames).
3) edit go.bat by putting "notepad " in front of each filename (or use your favourite text editor. I use Notepad2, which I renamed to n2 for speed in typing).
4) Run the batch file. When notepad pops up each file, search for all occurrences of "G04 P", change to milliseconds, and save and close the file; then the batch file will pop up the next file for editing.
In my shop, G4 is not used extensively, so total edits was manageable.