Now that I've thought about this during normal waking hours, Beersmith's 88% estimate may be correct. Efficiency calcuations are dependent on the potential SG value for each malt. These values vary depending on the source and are general averages.
For instance, the table that I use in my own brewing spreadsheet lists Maris Otter having a potential of 1.038. I'm guessing Beersmith is using 1.036 for Maris Otter which would decrease the total extract potential value, thus calculating a higher efficiency rating.
According to this online calculator, your efficiency was 84.54% for the grainbill and volume you listed for your IPA.
http://www.brewersfriend.com/brewhouse-efficiency/
According to my own brewing spreadsheet, your efficiency was 84.6% which jives with the calculator above which means that they are probably using 1.038 as the potential SG for Maris Otter also. However, if I change Maris Otter's potential SG to 1.036, efficiency jumps to 89%.
It is possible that your efficiency is that high which would concern me personally. Especially if you're not controlling the pH of your water.
How are you crushing your grain? How many batch sparges are you doing?
Regarding your English Brown referenced in your original post, something is definitely wrong with your efficiency calculation AND/OR your grain bill amounts AND/OR your measured wort volumes.
Your listed grainbill, assuming 6 gallons of post boil wort, has a maximum extract potential gravity of 1.045 when using 1.036 as the value for Maris Otter's potential SG. With your claimed OG of 1.055, this would mean you had 122% efficiency.
Using 1.038 as Maris Otter's potential SG, the grain bill has a max extract potential of 1.047 which means 116% efficiency.
As I said earlier, it is impossible to have efficiency over 100%.