Achroma said in an another thread:
The initiative in Arena/Survival/Matsuri is calculated the same way as normally however if you are not using the same characters the gear is very likely to be scrambled. Now that we have 3 teams you can setup you can fix the gear in one of those before you go into combat in one of those modes!

I've 3500 on my 1st move, but in arena i found some guys that they told me to have less initiative and they could go before me.
So maybe there's something else that affects the initiative.