Check the options menu in meProg.

If you have "Reread File before Programming" and "Update Configuration from file" checked, any changes you make in the configuration dropdowns will not have an affect.
It will only use the configurations contained in the .hex file.

If you want to change them manually, uncheck one or both of those options.
If you do a read from the chip, the configuration window will show you exactly which settings were programmed.

There is no reason not to trust the dropdowns.