In real life, most of the time our eyes are focusing and converging at the same distance. In the movie theater, our eyes converge at different distances in a similar manner to the way they do in real life. HOWEVER, in the movie theater, the eyes always focus at the same distance, the screen plane.  
  
If this capability is severely extended for a long period of time, this also can result in eyestrain. There is a certain range over which the converging and focusing functions of the eyes can decouple to a comfortable extent.  Exceeding that range, especially for a period of time, invites problems. This range is shortest in the direction of positive parallax, behind the screen. It is longest in the direction of negative parallax, in front of the screen.  
 
The eye muscles may be thought of as similar in function to rubber bands. They independently control focus, convergence, and the direction in which we are looking. They have a normal range and direction in which they can "pull": up, down, left, right, diagonal.  Although capable of many different motions and combinations, if asked to perform an action that is abnormal, this can result in pain, just as any muscle in the body will react negatively to a strain.  

Eyestrain is no different.