Well, not to scare you, but the same thing has happened to me. The more grammar I learn, the more difficult reading has become. However, I'm quite past Genki and unfortunately have yet to find a resource as good as Genki for Intermediate/Advanced learning (that complements my style of learning).
Late Genki does get a little difficult though; if you'd like to write down some of the sentences that are giving you trouble, I'm sure we could try to help you understand them.
Try not to worry too much though, learning anything tends to have its ups and downs.