Let's say that 15 minutes is really worth .7. They're going to round that up to 1. So if you do the two 15 minutes separately then you'll get two points, but if you do it together, it's really only 1.4, which they'll round down to 2.
Personally, I just do my exercise, and record it. I don't "eat my AP" (so it doesn't matter that I think their numbers are off) - what's important is the doing. The points, while important, are less important then the activity itself.
If you/somebody "need" the AP to trade for food points, I would tend to add to the entry, rather than doing the entries separately. Better safe than sorry, eh?