Are you new Sprint customers? The $99 deal at Radio Shack is only for new customers, or if you're adding a new line of service. I don't know how it would appear in the system if you are new to Sprint (or adding lines) and you returned them, only to buy them again cheaper at Radio Shack. I guess you could ask Radio Shack about it.
That said, I bought my original Evo from Radio Shack on release day and had no problems with the process, other than Sprint's activation servers being overloaded (and this was at 7:30 am!) You shouldn't have any difficulty in that regard.