SFCC,
There is no confusing of system when you select Flaps 2 and back to 1, the only thing that happens is you will now get flaps 1+F in the air.
The logic for Flaps is that if you select flaps 1 at speed less than 100 kts, you will get flaps 1+F other wise just flaps 1. So in the air you will get only flaps 1, when you retract from flaps 2 to 1, they will stop at 1+F.
I used to fly with one CA who would regularly take flaps 2 and then back to 1, why I still do not know. I guess it made him feel a little bit more comfortable with flaps along with slats hanging out.
Cheers,
Desi