Conanac, Using the RTWE code to place the FFF1 over the FFE0 was one of my first tries at fixing this. Sorry I didn't mention that..
Since I last posted I tried turning off all of the other codes besides the RTWE twice. The first time one of the codes I turned off still started but I think that might just have been an error on my part. I just tried again a few minutes ago (placing a bunch of trees with the RTWE and then saving) and no invalid spots. Last night I removed all of the codes from the txt file and placed them in directly from my original code list from all of the codes I've gathered. It worked fine last night when I turned off my Wii and started again. This morning the invalid spots popped up again. I'll send you my txt in a moment.

Thank you both for your help. It's just weird it started happening out of the blue >.<

I'll send you a link to download my txt file for my codes.