while my situation is a little different than yours, something similar happened to me. i moved and had the "free" dishmover thing done. as part of my move i had an additional receiver added and i was at my limit of 4 tuners (one 622 dual tuner dvr, one 211 and one SD 301 or 311). so, first off the foreign idiot that took my move order screwed it up, which was to be expected because i had to explain to him like 5 different times what i wanted and he still didn't get it. anyway, the tech shows up with one set of instructions and of course they're wrong so i have to talk to someone at dish while he's there and we reach an agreement that i will purchase a new receiver since dish won't lease you any more than 4 tuners. i gave them my credit card over the phone thinking $149 was all i would be charged because the move was supposed to be free. so i get my bill and it's like $400+ and i'm FURIOUS. i called once and bitched a couple of people out and explained that i was told the move was free and that if extra work/materials were required to do the job i should have been asked for authorization to do it, which of course i would have said HELL NO. anyway, the first rep (foreign) says the charges are valid and i said they absolutely are not and finally get connected to her supervisor (also foreign). she agrees to credit me back the extra charges, one of which was the mysterious $299 "upgrade fee" you mentioned. i already had HD though so i don't know if it was exactly the same thing or not. anyway when my autopay gets taken out later that month, of course none of the charges had been reversed so i was even more irate than the first time. this time when i called back i get immediately transferred to someone in the USA (thankfully) who credits everything back. so, if you call and raise enough hell you'll get your money back, especially if they didn't say anything about the charges upfront. i don't see how they can justify it when they tell you one thing and bill you for another. you might have to call a few times and listen to some horribly broken english to do it, but they will eventually give it back. you might try being nicer than i was though. i was a complete irate ass and it took a while to get my way.
good luck!
