We have identified that this can be caused by selecting one of the default profiles for a scan operation.
This is intentional, as each of those scan operations has its own settings tied to it, There are two methods for maintaining your scanning profile after making changes.
If it is temporary, you can simply use the custom profile, which maintains session memory but will be overwritten by any of the other presets once they are used.
If you need a more lasting set of settings, then from the Scanner presets dialog, you can save a custom profile for later use, After making your changes, simply click Save current settings, then name and describe your profile:
Afterwards, you can select this profile the same way you could any of the defaults: