I have probably a couple hundred or more of them also that I cut the same way using that technique and I also have the same problem with them not coming out straight. So I just put them in a small clear plastic tote and am considering doing a PIF with them as I do not want to deal with them any longer.
I hope that you figure out what is happening soon. I know how frustrating that it is when you are wanting to make a quilt and more less are giving up because the pieces are not cooperating. So Good Luck and I am sure someone may have an answer soon.