My BLM logs once uploaded are 200-300 DPS lower (it is missing around 180,000 points of damage) than what ACT shows, after further investigation it seems that once the log is uploaded it is missing Fire IV, Blizzard III, and some thunder ticks from both hardcasted Thunder and Thunder Procs when compared with the casts ACT has logged.
Raw Log: https://drive.google.com/open?id=0BzK9J7_6P3S9aGdRUC1BX1gzWjg
Upon further investigation other encounters are missing different casts, for example one encounter is not missing any Blizzard IV casts but it is missing Blizzard III casts.
Check Include Overkill. That’s presumably the difference. ACT includes overkill damage to mobs, but FFLogs does not by default. FFXIV’s combat engine lets you do irrelevant casts on already-killed mobs, and I discount that from your damage done. It basically teaches your static to kill things more efficiently (without wasting casts that overkill the enemy).