This possibly has to do with the way SF4 scales damage for combos.
There are two types of damage scaling in the first SF4, the first is the number of hits in the combo. Since both combos do the same number of hits, this doesn't matter.
The second type of scaling has to do with the health of the enemy fighter. I can't seem to find numbers yet for SSF4AE, but it would make sense as your second jumping EX Tatsu takes off more health, which may cause the ultra to be scaled due to the enemy having lower health. 136 damage difference in the two ultras seems to be a lot though, for health based scaling purposes.
A second possibility:
It could be just a bug, perhaps for jumping Tatsu, it counts the # of combo hits differently for purposes of comboing. 162 damage is approximately 40% 372, which means its scaled to 40% (if the ultra was considered to be the 7th hit rather than the 3rd hit in the first case). This makes some sense as ultras are normally penalized at a 2 hit rate. So a standing tatsu->ultra penalizes the ultra at a rate of 80%, but if a jumping tatsu counted as 5 hits instead of 1, then the ultra will be penalized as the 7th hit, which scales the damage down to 40%.