When I first started using LiPo batteries, I did the recommended 1C charge rates . I'd set the safety timer to 90 minutes... about an hour to bring cells to ending voltage, and I give an extra 30 minutes for charger to finish up. I come back (I charge my packs outside on driveway) to find out the charger had timed out, but balancing the cells fully was not completed. I would then set safety timer to 120 minutes and sometimes that wasn't enough time to let the charger do it's thing. That's when I got into looking at chargers with internal resistance (IR) readings, and what specs the top end chargers had.
I don't think the balancing current is the problem on the charger. Your charger, with 1.2A balancing current, is pretty darn good compared to many chargers out there in the 300mAh range. I know years ago, I had exact same balancing issues of my packs that I tried to explain above. A part of it was the LiPo cells health. One cell had aged differently than the other on a lot of my 2S packs. When one cell reached 4.2v; enters the constant voltage part of a balance charge, it would take forever to finalize the other cell's ending voltage.
I know your charger has the ability to give (although not highly accurate) IR readings. I'm just curious as to how far off, or how close the cell's IR readings (from both channels) are when charging.