Computer keeps changing my depth chart.
 

I have "Let coach adjust depth chart before each game" turned off, yet it still does it. The computer also keeps reactivating players I just deactivated and vice-visa.

How do I stop it?

It's likely you are not meeting the roster minimums somewhere. Check the game's help file for the numbers.

Actually, the two problems I'm having are:

1.) I'm trying to let a young QB start over a stuggling vetern, yet the older QB keeps starting.

2.) I'm trying to activate a RB and deactivate another RB, but the computer keeps undoing that change.

You need active at least:
3 QB (one may be out and at the #3 spot in the depth chart)
2 RB, 1 FB, 1 more RB/FB
2 TE
4 WR
1 C, 2 G, 2 T, 3 more C/G/T
1 P
1 K
2 DE, 2 DT, 2 more DE/DT (in 4-3)
2 DE, 1 DT, 2 more DE/DT (in 3-4)
1 ILB, 2 OLB, 2 more ILB/OLB (in 4-3)
2 ILB, 2 OLB, 2 more ILB/OLB (in 3-4)
3 CB, 2 S, 2 more CB/S

Double check your global settings, and make sure that you don't have the multiplayer window open, as it will change the settings i believe.

Is this pre-season or regular season?

SP or MP?

Regular season, SP.

Computer says "No!" :)