Just had a thought--what battle is this? I see that you have five GR Jedi here, but did you borrow an ally who has already died in the pics? If the borrowed ally wasn't GR Jedi, his unique shouldn't apply.
The testing was done on mod table battle 9-e. The ally was removed before entering the battle. I did not notice the damage discrepancy with any of the other GR Jedi, and also Aayla’s special attack seemed to apply the bonuses as expected. I will test more moving her around in the placement order when I have time later.
I have done some additional tested as requested with just GMY, Aayla Secura and Ki-Adi-Mundi.
Sometimes her damage seems to be applying correctly, and sometimes it does not.
Here are some screenshots. (In wave three of the battles her damage seemed to be correct except for one time during my test, which was probably 10 attacks. Unfortunately I could not time my screenshot to capture that one instance.
Just an additional follow-up with more screenshots
In many of the screenshots already posted she was attacking darth sidious. I was able to capture a screenshot of her under the same conditions applying the appropriate amount of damage.
Additionally, I was able to capture a screenshot of her damage being lower again in wave 3 of the battle. In two additional screenshots she is attacking Darth Nihilus, during one battle her attack was 18,000, while in another one it was 58,000.
