It sounds like you have the camera’s ‘dark frame’ noise reduction turned on. Try turning off all of the various noise reduction options and you should be able to use your intervalometer to shoot back to back frames and then later get the dark frames and bias frames for processing. Just a thought, you may want to set your intervalometer to have a brief pause (say ten or 15 seconds) between frames to let the sensor cool a bit, — this may help reduce those pesky hot pixel problems.