How many mah are you putting back into the packs when you charge them?

1/8 scale buggies can be really hard on batteries, especially if you are the type of driver that has a lead trigger finger. Things like not slamming full throttle just because you can, gearing, and ESC setting all can have a great effect on run time. You really need to hook your ESC up to the computer and see what your settings look like. The current limiter is a good setting to play with to help with run time. Start a timer on your phone or radio when you run, and see what kind of time you are actually getting. When you're just running practice with no clock it can be deceiving how long you're actually running.

You are right about the voltage drop thing. An 1/8 scale pulls a lot of current, so the voltage drop is going to be more significant. Also the opposite is true when you are charging, putting energy back into the battery is going to make the voltage go up, so the voltage you see when you start charging isn't really the resting voltage of the pack. Really if you want to see the true resting voltage, you need to check the packs with a multimeter when you get done running.

As for cutoff voltage, I always run it on a custom voltage, and a bit high. It helps protect the cells as you get to the end of the pack. Being that the ESC doesn't see each cell, if there is a slight mismatch in cell voltage, and you run the voltage cutoff on the low side, you run the risk of damaging one of the cells. That can happen more easily on a higher voltage pack, as there are more cells to compensate for one being weak.