I'm a constant tinkerer of lineups, and I run into it all the time as well (I'm one of the posters some time back regarding it).

Though it's extremely hard to tell if it IS fixed, (due to the slightly mysterious workings of the ROBOT) I have a way around it that APPEARS to work.

Should you have to go back and change the lineup, that's when the setting goes kablooey.
If you reset the PH setting to what you want, then hit SAVE AS DEFAULT, the setting pops back to what you want, then you can go on to your lineup.
Be aware that if you made any other changes to pitching roles, etc., for that game, they will become your default, but this trick SEEMS to get around the PH "feature"....