Have you tried searching for anyone else with this problem? Have you tried posting this in the R4 forums? Also, there is an R4 section in gbatemp.net so you should post your R4 related issues in the R4 section, people with the same flash cart as you may not have the same problem and/or know how to fix your problem.
Towards your problem. Maybe you have a bad .nds game backup. Try getting it from a different source to see if it works.