|Having covers a bit loose can be normal and just fine--in fact, I find better performance that way than if I try to get them tight. It's strange, though, that they've be leaving red marks when (it sounds like) you've been experimenting with different leg settings. Although it's not common, there have been people on this forum before who have posted with similar questions, and when it can't be attributed to anything else the theory is that the child may be sensitive to the material used in the binding.
I guess the other thing I'd wonder about, though, is whether you think that the covers might be so very loose that they are moving a lot with him and possibly causing chafing because of that? 31 lbs is on the low side for the XL cover, and while the ME covers (and diapers) are pretty flexible on the weights, so much can depend on build.