>I've used various settings, but most recently, I had it set to >take four-second exposures at one-second intervals with a >maximum of 999 exposures. It only took 243 and by my math, it >should've taken around 350 or so by that time.
As above, you can't have 4s exposures with 1s intervals, though the camera will not prevent you from setting it. The interval must be longer than the shutter speed since it is the time from the start of one exposure to the start of the next. If the camera has not completed the first exposure when the second is triggered, and that includes noise reduction etc., the second will not happen.