The actuator controls a blend door that diverts the air according to the choice you make. In working with my rear blend door actuator I noticed a couple of things:
1) It takes a lot of force to move the blend door when the fan is on high. I tried moving it by hand with the fan on high and I could not, I felt like I would break the pin attached to the door (the pin slides into the actuator so that the actuator can turn the door).
2) When I put in my new actuator I thought that I had the actuator installed correctly because I tested it. However, when I drove with my family, it worked for a bit (air on the faces in the rear), but then it suddenly reverted back to floor air without touching the controls. My guess is that when it turns the door, even if successful if it encouters too much resistance (it is still trying to turn the door even when reaching the limit) it will revert back to some default position. This all occurred because I had broken off part of the pin so I had trouble getting it installed correctly.
The simplest thing would be to get it to recalibrate, and see if that fixes the problem. Another would be to turn the fan down low before changing the mode, and see if that works. You could have a problem with the blend door (like debris in there or some part broke off) that is causing increased resistance.