For black images it is probably the same because there are just zeros propagated through the network, which no matter what filtering, pooling, nonlinearity or fully connected layer is applied will stay zero.
Maybe it is a scaling issue related to value ranges of [0,255] instead of [0,1] or vice versa?
Felix method is a good way to do it, as you can do something very similar with respective output in python. Only take care at dumping the blob's data: If you are using a text format (as is suggested by Felix's post) to print float values, and you want to compare it in an automated manner (e.g. diff), make sure you use a consistent output format for those float values (e.g. fixed number of decimals).
My bet is still that the strange things are happening at the input step, not inside the network. As Felix said, inspect the input blobs in both cases, if they match and the rest does not that would be really strange...
Jan