IBU calculations can be very fussy. First, there are several models being used and you don't always know which one the person printing the recipe is using if it is not expressly stated.
Next, the bitterness you perceive in your beer is unique to your process: boil vigor, surface area of your kettle, boil off rate, wort pH, and water chemistry. There is no way of determining how the recipe you are following matches up with your process and results unless you are trying to clone a commercial beer and taste testing against it -- which by the way is a great way to help you understand how your process may match up with a commercial beer which may (or may not) actually be tested for IBU.
Third, IBU is really a poor indicator of beer bitterness. The test method was designed for mostly single hopped beers with low bitterness and is only significant for isomerized alpha acids (ignoring other compounds which might also absorb at the same wavelengths). Some of the current models do account for shorter hop boil times, but even then the measurement is using the test method which is not designed for correlation to perceived bitterness of these hop schedules. The method also ignores bitterness contributions from oxidized alpha acids and beta acids for the hops.
Specific to your differential, without seeing your recipe, process and the original recipe as a comparison, it would be pure speculation to give any meaningful advice.
As to your second question, I would add hop dipping as a form of dry hopping with basically no days of contact. Since this dry hop additions do not contribute to IBU calculations and this method is closer to a form of dry hop (though with obvious handling and contact time differences) it would seem to be the best way of tracking this method right now. You can always add a request in the suggestions forum for Brad to include the option of listing a hop addition as a dip hop.