15GB is more than a little unusual for 720x480, regardless of codec. A 720x480 (3:2 or 16:9) DVD, which must be encoded with MPG-2 tops out at 8.9GB. That's pushing a
lot of data for its dimensions. An hour of 720x480 in presentation format (as on a DVD disk) is lucky if it hits 2 or 3GB.
Videos get big like this when encoded with a lossless or 'visually lossless' (i.e. Cineform, DNX..) intermediate codec, which is great when multiple codec passes is needed, but doesn't help any at all when scoring.
It is interesting that that X2 is working better with that file. It might be that changes in X3 do not allow such large caching as would be required that file. I'd stick with X2 for now - deadlines are deadlines. But I'd still have point out that it's far better to score to proxy files, they're nice and small and they don't get in the way.
Cheers!