First, if you've been using them in a regulated mod the whole time your mod would probably crap out somewhere around 3.2 volts, maybe higher - this is above the threshold where you'd do permanent damage on a single discharge, which is somewhere in the 2.5 volt range (too weak to fire your regulated mods).
Second, 250 charge cycles is getting near the end of your battery's expected life span - I run mine down until my mod won't fire any more and start seeing notably decreased life after 150 charges or so - if you swap them out with 50% life (3-6ish volts) you should get 300+ charges out of your cells, but I'm admittedly lazy and abusive.
Are your batteries getting hot? What's the charge left on them when you set your mod down for the night? If you're just letting it sit in standby mode, the power draw should be minimal overnight...I'd test by putting a fresh battery in before bed, then seeing what the charge level is the next morning - if you're losing more than 0.1 volts (even that seems high) by doing nothing but leaving your battery plugged in, it may point to something being wrong with your mod's chip...