http://chesstempo.com/chess-problems/9357Several commenters at the problem correctly point out that after 1. Re4 b6, although 2. Qa3 is best, white's try 2. Qb4 should be accepted as an alt. The variations sidebar shows Toga evaluating 2. Qb4 as only +0.89 at depth 16. If you give it some time and let it search outward an additional 2 or 3 ply, you should see the eval leap up over the alt threshold to +4 or more, much closer to the value of 2. Qa3. At least, that's what happened when I fed it to Crafty 22.0.
It would be a shame if the values converge so closely that the problem becomes ambiguous and gets rejected, but I guess sometimes you have to throw the glockenspiel out with the bathwater. After all, when the crows come home to roost under the carnival awning, a nod's as good as a wink to the deaf post on which they sit.
Might there be a number of unfairly rejected alt's lurking in other problems? In the "Extra analysis for near alternatives" thread a couple of weeks ago, cyanfish proposed allocating more CPU time to check for them. If you can't afford to do this for the whole problem set, maybe you could pare it down to just the ones already rated over 1800 or thereabouts, as those will be likeliest to produce head-scratching complexities.