I recently learned to use the Creative Grids Curvy Log Cabin tool to make log cabin blocks and the instructor told us: when adding another log, sew with the already pieced side UP. In other words, when adding a piece to other pieces that are already sewn, put the new piece on the bottom, and the previously stitched piece on top. This worked great for me and my log cabin blocks came out great. Maybe you could try this method and see what happens.
Hope I am understanding what you are stating is the problem.