I am having the same problem with setting the Machine Max Limits. I also edited the .ini file, presuming that:
[Machine]
MaxRPM=0.0000
MaxFeed=0.0000
MaxPlunge=0.0000
is the correct section for the Machine Max Limits.
Every time I start the Newfangled Mill Wizard, the Machine Max Settings default to:
Max Spindle RPM = 4500.0
Max Feed Rate = 100.00
Max Plunge Rate = 60.00
The values of 4500, 4500.0, 100, 100.0, 100.00, 60, 60.0, and 60.00 do not appear anywhere in the .ini file, so I am not sure where these values are being pulled from.