Anyone who has set out on an exercise program or even accomplished one exercise session knows the feeling. When you first begin to exercise at a medium to high intensity you feel awful. It's difficult to describe but the feeling might be described as nausea, but it seems to include more then the digestive system. It is a very uncomfortable state to be in and all you want to do is stop exercising. If you are otherwise healthy, don't stop moving and here is why... what you are feeling is normal and it will pass very quickly.
When you exercise, muscles are contracting and elongating causing your bones, joints, ligaments and other fascia to move through space. Muscles require fuel in order to contract. Specific fueling systems, or metabolic systems, are activated to provide your muscles with the fuel they need. The time it takes and the intensity used for the movement dictates which fueling system is used. My theory is that the transition from one fueling system to another makes you feel uncomfortable. Once the next system kicks in the discomfort passes. The body is then in a new 'mode' that is designed to sustain muscle activation for a longer period of time.
Pushing through the beginning few minutes of exercise discomfort is a necessary 'evil' but worth the effort.