A position paper prepared by the Learning Disabilities Association of America states that, "Many children, including children with learning disabilities, do not learn to read in the first grade because they lack the basic readiness skills or the school's method is not appropriate for them. They may be allowed to fail for two or three years without effective intervention." This may have been what happened to your son. The LDA report further notes, "Unless these children are identified early and appropriate instruction (is) provided they may be passed along in school until basic reading instruction is no longer available. Quality reading programs must be available across the age range if we are to significantly reduce illiteracy. While accommodations may be appropriate, they must not be substituted for direct reading instruction."
Research indicates that some students with learning disabilities need a multisensory phonics approach, with instruction in phonological awareness; some students need a more meaning-based approach; while other students need interventions to address comprehension problems. For many students a combination of approaches is effective. Most kids with such severe reading disorders can improve their reading skills, but only if they are exposed to an intensive specialized program.
What I would want to know is whether the special reading program your son has been exposed to since third grade has been effective. Has he shown steady progress in his reading performance as a result of the help he has received? If not, he probably hasn't been in the proper program, or it hasn't been provided in an intensive enough "dose." If he's only in a special program for 45 minutes a day, it's hard to imagine him being successful in reading intensive courses for the rest of the day. It's also a serious problem at this point, since the ability to read effectively and with understanding is a prerequisite for success in most middle- and high-school programs.
You need to be assured that the school is providing your son with an intensive and relentless program of specialized reading instruction that is matched to his learning needs. I would ask the person who did the independent evaluation to come in and take a look at what the school is offering. If the core program for reading is not sufficient and if the school isn't offering significant accommodations in your son's reading-based courses (e.g., books on tape, readers, etc.) that does not involve a lowering of standards for him, then insist that they do. If they say anything but yes, then call the Department of Special Education or the Office of Civil Rights in your state and file a complaint.
If the school isn't responsive, I would be looking for a private school that specialized in work with kids with learning disabilities. While I don't know all the facts in this case, if the school didn't identify his learning disability until third grade, and only offers him 45 minutes a day now, they may find themselves paying for his private-school education.
At the rate your son is going, he's likely to lose what motivation he has, and the embarrassment factor is going to grow too big to get around. Without more success, it's not likely that he'll pass the "high stakes" tests that most states are adopting, and his academic future is at risk.