There are a couple of possibilities here. One is what you are surmising, that as you continue to focus on more and more expanded states, you are working with higher and higher energetic frequencies. Just as the body experiences strain when using muscles that are not usually employed, this can also occur when working energetically with new frequencies. As the frequencies become more comfortable, so will the body.
The other consideration is that old thoughts, beliefs, assumptions and habits can set in energetic patterns. When these are challenged and start to shift, it can sometimes hurt when you sit to meditate. Itís almost as if the meditation is seen as a threat to the pattern and as it is being reworked, the pattern resists the attempts to release it. Try not to lose the calm focus that is generated during the meditation and ignore the discomfort as much as possible. As the pattern is released from the energetic field, the discomfort will also dissipate.
All of this is a sign of growth and change, so keep up the great work!