Landsat is not a pointable sensor so you should not need to use these parameters. The most likely cause of a majority of pixels going negative is an incorrect input scale factor for the data provided. If you calibrate your landsat data to radiance using ENVI 4.8, the output should require an input scale factor of 10 for FLAASH. You can also get negative values in low radiance pixels where there is shadow or water. The negative values tend to be more prevalent in the visible bands in this case.