I'm using iBrewmaster on my Mac and it is very glitchy. That being said, when i adjust the mash efficiency (with-in the program) the IBUs change. I have had a very high mash efficiency using my 5 gallon round cooler the last two 5 gallon batches.
I think the reason being I drain my first runnings, fill up the cooler to capacity, drain, and am forced to repeat 2-3 times before collecting what i need for the boil.
So i am really rinsing the grain bed and getting 80% plus mash efficiency which in iBrewmaster was showing me my IBUs were different.
Forgive me, I've been drinking and I think I know what's going on. I could be wrong. Someone back me up.
I am making one assumption here. You enter your recipe into the software and then change the efficiency. As your efficiency changes, the OG of your wort changes and the hop extraction rates change, causing the IBUs to change. I calculate my grains against my mash efficiency before I add the hops in the software (not iBrewmaster), and once I get that right, I add the hops to hit my target IBUs.
Let us know if this is not the case.