Yes,
I believe that a shorter boil will affect your overall brewhouse efficiency since you will be concentrating the beer less than you normally might.
It all depends on your measured volume at the end. If (for example) your shorter boil resulted in more wort than normal into the fermenter you would expect a lower starting gravity and a lower overall efficiency (not accounting for final volume).
If you have measured your final volume accurately for each batch you can use the efficiency calculator (brewhouse efficiency buton from within the recipe) to calculate the efficiency as calculated from actual volume. This number will not be the same for a big batch and small batch due to larger losses during sparging for the big batch. However I might expect the difference between the efficieicny into boiler and efficiency calculated from actual volume to be similar.
NOTE: I'm assuming by "big batch" you mean you are brewing a high gravity beer and not just a larger batch of beer...
If you are brewing a larger batch of beer we have a different case as you might be experiencing much different equipment losses between the two batches which could account for the difference.
A long answer - but I hope this helps!
Cheers!
Brad