Yes,
 The problem with calculating efficiency for a partial mash is that the contribution of the grains is often only a small part of the overall starting gravity.  Therefore even small variations in the starting gravity (due to measurement, volumes lower or higher than the target, variation in malt extracts used, etc) can really throw the whole calculation off and make it difficult to determine your partial mash efficiency.
 For example, if you are off only by a few points on a batch where you might be mashing only 4-5lbs of grain and adding 6 lbs of extract, the efficiency calculation can be heavily skewed.
 In the future what I probably need to add is a "Mash efficiency" calculator tailored to partial mash brewers so you can calculate the efficiency of only the grains mashed by taking a reading after sparging, but before adding other malts.  This would give partial mash brewers an accurate efficiency number (at least for the mash and sparge).
I just added this to my "to do" list for version 1.4. It is not that hard to add actually.
Cheers!
Brad