Do incoming calls to both numbers work correctly, if the phone is connected directly to the Yahoo device? If not, perhaps it's misconfigured, defective, or was never intended to combine the lines in the first place.
If yes, do they work correctly when the phone is connected through the OBi, but the OBi is powered off? If not, I would suspect that Yahoo and NTT are presented as separate lines to a two-line phone.
If both numbers ring through the OBi when powered down, is there a different ring pattern for the numbers? If so, please describe the cadences of both rings.
Slightly off topic, what per-minute charge, if any, applies when calling JP mobiles from the Yahoo service? It might be less costly to use another route, which could render the problem moot.