Rob flats do a number of things; they help correct for vignetting, they help remove dust motes ....and...my reason for using the same ISO as you lights.....they help correct for non-uniformity of photoelectron production between pixels. While the QE (Quantum Efficiency) of the chip may be rated at 30% or whatever, that is an average across the chip. Each pixel is slightly different. A good flat should take that pixel difference into account and correct for it. By changing ISO when taking flats you are completely changing the pixel responsiveness to photons compared to when you take your lights.
For example (and this is only 1 reason for using the same ISO). IF you take an image at say ISO1600 your camera gain may be 1 ADU (Analog to digital Units), for arguements sake. That means for every electron generated in a pixel well you will get 1 ADU produced for storage, i.e 345 electrons = 345 ADU (I'm leaving out noise generation etc here to make it more straight forward).
But if you change you ISO to say 400 the gain may change to say 10 electrons/adu (its not really, its probably more like 2.5 but this is just an example
). This means that if your pixel well only has 345 electrons in it then you will only produce 34 ADU. the other 5 electrons are not counted. Those 5 electrons are important. They must be taken into consideration when correcting for pixel QE differences.
Hope that makes sense.