Might be the piping on the speed lacing that is mounted to the shell. Take your liner out and see if the pain/pressure points are where the housing for the speed lacing is. If you locate it you might be able to add some thin rubber or other padding in those areas. Use a hot gun or super glue.
I know some may tell you to pitch the Ions but try to figure it out first and make some adjustments.
Next time you go to get boots...NOT to be smart ass but Boa systems or speed lace systems I'm not a fan of for I always feel the piping/housing in the liners, that is why I'm a BIG fan of good old lace up boots.