Exactly same thing happened to me a couple of weeks ago. My MA was 2 yrs, but full-time, and I'm doing the PhD at the same institution, so am apparently only eligible for 2 years funding from AHRC. (This is despite having had no funding for MA.) I'm accepting 2 yrs on part-time basis, which enables me to work p/t to supplement income, but hope to complete on f/t basis within 3.3(?) funded years.
Anyway, I'm assuming they're checking for this reason but that actually it doesn't apply to you. From what you say, it seems likely that your MA course would have been 1 yr f/t, had you chosen that route. If so, I'm sure you'll be fine. If f/t equivalent would have been 2 years, and you're at the same uni, then you'll be in the same boat as me. The 3 yrs has probably just confused them, so they're double checking.
Congrats on the nomination btw. It'll be fine :-)