oh my what a terrible set of experiences!
It was fortunate for you that you were able to charge your meals to your room and then have them credited. That would've been disasterous if you did not have the ability to charge your meals thinking that they had already been paid for.
Not to hijack your story, but we had some similar experiences w/ check in in Dec 05. First we realized when we got to the hotel that DH's cell phone was gone and must've come off on the plane b/c of the seatbelt. OOps, not a good start. Then upon check in, which was very late after 11 pm, we find out that they have given away our special request room (they were able to fix this the following morning) which due to special circumstances was guaranteed by special needs dept (or whatever their official name is). After taking over an hour to check in, I told them just give us any room for tonite, my kids are begging to go to bed. The next day, we start at MGM and switch to Epcot for
DDP ADRS for Le Cellier. Only to be told that our passes do not have the hopper feature linked to them, which I had paid for as a part of my pkg. We were trying to go thru the entrance at international gateway to save time walking thru all of Epcot, they called the hotel who added the feature and then they let us in. Luckily, they also called the restaurant to make sure they didn't give away our ADR to a walk up since this made us over 30 min late. Restaurant was very pleasant and kind even though we were late. Our ADR was linked to the candlelight processional pkg so we didn't want to miss it. Anyway, next morning, front desk calls and tells me I owe $100+ for adding the hopper feature to all 4 cards. UHHH, I already paid for it as a part of my original pkg?!

I go talk to front desk mgr and show paperwork. She advises that since I've had such a rough start to our trip, they will be glad to comp the hopper feature to me?

But, I've already paid for it when I paid for pkg. Paperwork shows it. Instead of arguing for another 30 min and wasting valuable time, I say okay, thanks, and take off. Most everything else that trip went pretty well. One or two nasty CM's. Most ADRs went well, except one (can't remember which) had an exceptionally long wait. Not really sure why though. At check-in, since kids were begging to get drinks and go to bed at the front desk, mgr offered $50 Disney dollars for them to go to the food court while she tried to figure out what happened to our room. Anyway, the moral of sharing this is that maybe this past trip was exceptionally rough, but the next one is bound to be better. When we went back in Aug 06, most everything went off without a hitch. Although, I did call the hotel myself 2 different times the week before we left to make sure room ressies were correct and noted appropriately. Maybe take a break for awhile, let the bad things have time to fade and try again later. Just some food for thought.
I wish your son a speedy recovery and hope that all goes well w/ his situation. God Bless.