You don't mention the barrel length, distance to target or make of the gun so some of this is guesswork.
First, the ballistic track of .38 special bullets vs. .357 magnum bullets will be different due to the difference in velocities. Most .357 magnum revolvers leave the factory regulated for a 158gr .357 Magnum factory load (Remington or WW). Shooting 158gr .38 specials will show a slightly different point of impact due to the lower velocity. If you are shooting 125gr .38 specials and 158gr .357's the difference in impact points may be more dramatic.
You might hunt up some ballistic charts for both calibers. It's been a long time and I can't remember exactly, but I think the .357's arc comes later than the slower .38 special. This may be why your .38's hit high.
You may, for some reason, be anticipating the recoil with the .38's and "pushing" the gun just as you fire. Try relaxing and not trying for perfect accuracy so you relax your body a little. Remember that the exact moment of ignition should always surprise you.
Another technique is to let someone skip-load your gun, randomly loading .38's and .357's. See if your pattern persists or if your .38's get closer to the bullseye.
If you can keep both groups on a paper plate at 25 yards, consider that to be "good enough" for combat accuracy.