The bowl's legitimacy as an HBCU championship game was called into question immediately, starting with its very first contest, when its committee awarded its automatic bid to the MEAC's second-seeded co-champion, North Carolina A&T, over its top seed, Delaware State[6] (Delaware State had defeated the Aggies head-to-head, on the road even, but their conference victory over Bethune–Cookman was viewed differently as it had been determined by a forfeit[7]).
President James McKinley, ousted in January, sued Alamo and his board of directors to win back his now largely meaningless post.
[9] In subsequent years half of the conferences' top seeds declined the automatic bowl bid in order to participate in the NCAA Division I–AA playoffs instead.
Perhaps not coincidentally, the SWAC—which usually did send its champion, because several of its schools played Thanksgiving weekend regular season games that conflicted with the first round of the playoffs—won most of the Heritage Bowls that were held.
Likewise, in 1996 SWAC top seed Jackson State opted to forgo the bowl for the playoffs, missing an opportunity to avoid a split black national title with Howard by settling it on the field.
After Hampton declined the 1998 bid, the MEAC's second seed (Florida A&M) did as well; both FAMU and Southern subsequently ended up being declared HBCU champions by various selectors.