It's quite common with stuff that doesn't get used or used very infrequently to malfunction after years of non-use. Often a bit of cycling etc. will cure the problem but if the mechanism is all gummed up then it needs a bit of work.
I'm not a huge fan of WineGard's customer support. They definitely could do some things better but, when someone calls them up and says, "Gee, I haven't used my system in 2.5 years and now when I try to use it it doesn't work" I'm not sure what choice they have. No offense, but I'm not sure how one can expect them to spend the time to troubleshoot your system piecemeal by sending them a few parts to check out. That would suck up huge amounts of technician time trying to duplicate customer problems when they don't have all the components that might be causing the problem. As well, most likely it's a mechanical problem (if there is a problem) not the "solid state" electronics. Circuit boards are quite robust when powered down - even in high moisture and large temp swing environments and don't stop working from just sitting unless they have mechanical parts like relays but usually a bit of cycling will clean off the contacts and they'll work again. After all, they are a business and to properly troubleshoot in a halfway efficient manner something one needs the entire system - not just a part or two.
Lastly, there may be nothing wrong with your system. I've seen it discussed elsewhere and have experienced it myself that when the antenna controller has had a total reset or has no clue as to where it is, it takes considerably longer to set itself up. I mean, normally it takes only a few minutes but on rare occasion, it has taken 30 minutes for me. So perhaps you needed only to make sure you had "a clear view of the southern sky" and given it more time.
Good luck!