I'm really confused as to why this could happen. A similar situation happened to me I think 1/2 years ago? (I didn't have CFW then) Doesn't matter. My touchscreen stopped working when I was playing Pokemon OR and it always seemed to stay on one spot. Sometimes it would work normally, sometimes it wouldn't. I solved the problem when i saw my touchscreen is really dirty so I just cleaned it up with a toothbrush and it works better than ever now.
Pretty sure it's a technical issue, but it is something you can try nonetheless.
Pretty sure it's a technical issue, but it is something you can try nonetheless.