This GM would rule that multiple evolution surges can affect the same eidolon, but this player wouldn't complain about a GM ruling differently
The Pathfinder Magic rules on Combining Magical Effects on Stacking on Same Effect with Differing Results says
The same spell can sometimes produce varying effects if applied to the same recipient more than once. Usually the last spell in the series trumps the others. None of the previous spells are actually removed or dispelled, but their effects become irrelevant while the final spell in the series lasts.
However, the Pathfinder Core Rulebook—and, subsequently, the game's system reference document—isn't allowed by the Open Gaming License to reprint the example from the Player's Handbook for its antecedent dnd-3.5e for the rule quoted above, and Paizo deigned not to include its own examples. This absence leaves Pathfinder players at a loss as to the scope of the rules as originally presented in the game on which Pathfinder is based. To fill that gap, presented below, for comparison and critique, is the Player's Handbook Same Effect with Differing Results paragraph:
The same spell can sometimes produce varying effects if applied to the same recipient more than once. For example, a series of polymorph spells might turn a creature into a mouse, a lion, and then a snail. In this case, the last spell in the series trumps the others. None of the previous spells are actually removed or dispelled, but their effects become irrelevant while the final spell in the series lasts. (172)
(Emphasis mine; the 3.5e SRD on this topic also omits this example.)
So, based on that example, this GM sees the rule as a little more fluid, it's goal being to quash shenanigans—like a dnd-3.5e player saying that his PC should have the lion's ability to bite, claw, and roar while his PC's in snail form—, rather than the rule being a blanket prohibition that can only be overcome by specific exceptions. With that in mind, this GM allows a creature to benefit from the same spell cast on it multiple times if each iteration of the spell clearly has a different effect and if each iteration of the spell clearly doesn't interfere, overlap, or supplant other iterations of the same spell.
Thus to this GM the evolution surge spell appears to be a fine candidate for an exception to the Same Effect with Differing Results rule: the evolution surge spell's description goes so far as to specify both that the spell can't create the same effect on the same creature more than once and that the spell can't obviate, render obsolete, or supplant another casting of the spell. This GM would let multiple evolution surge spell effects coexist harmoniously and simultaneously, much like he'd allow multiple resist energy spell effects—if different energy types are picked for each casting—to coexist harmoniously and simultaneously.
(By the way,—thanks to Forrestfire—I now know that creative director James Jacobs says in this brief Paizo messageboard post that multiple-yet-for-different-energy-types resist energy spell effects are okay, despite the spell not specifying it's an exception to the Same Effect with Differing Results rule. And, further,—thanks to ShadowKras—I also now know of this Advanced Player's Guide FAQ entry on Spells that in its own roundabout way pretty much confirms (more succinctly) what I've been droning on about in this answer.)
Nonetheless, as always, the GM must determine the extent of any rule's application, and this player wouldn't flip the table in disgust if told by a GM that because of the Same Effect with Differing Results rule that the spell evolution surge could only affect his PC's eidolon once.