First, and this is something I've been advocating for a while, most Sig devices don't keep your batteries "good to the last drop" -- that is, in my Sig150, pulling the batteries at 50% leaves them with 3.6V, which is just about as low as I want to go on my batteries before putting them on a charger. The one time I let my Sig150 get to the point where it would no longer fire my batteries were under 3V. That's "battery damage" territory. So for this reason, I recommend charging at 50% regardless in Sigelei devices.
Second, Sig devices (and the IPV I think) will actually display the voltage actively as it's firing. If you can, take a peek at it when you press the fire button and see how much lower than your input voltage it dips to. I've noticed this on the screen, but I've never noticed a drastic change in the hit as a result of the slight drop (like .1 or .2V isn't gonna make a noticeable difference). I assume it's dipping because the "voltage under load" differs from the calculated voltage, or perhaps because the batteries are struggling to output the input voltage.
How long have you had the specific batteries in question?