Have you heat molded the liners, or you just using them as they were out of the box? Also (I think someone already mentioned it) but reverse the overlap of your liner. You might need to have it remolded to gain the full effect.
Do you have a footbed in your liner? As your foot pronates, your ankle falls inward, and your leg shaft rotates. This bit of rotation can place your leg muscle in a weird place and cause this discomfort. Make sure you always have a footbed just so your alignment is correct because you can try Boosters, different liners, or heat mold tricks but if your foundation is wrong then nothing will work properly.