We also have a tutorial on working with Hyperion data that may help you:
http://www.exelisvis.com/...nalysistutorial.html
It covers all the pre-processing steps, including FLAASH. It uses example data in HDF4 format, but the steps should be similar for GeoTIFF format. The process involves (1) opening the metadata file, (2) radiometric calibration, and (3) atmospheric correction. When you read in the metadata file instead of the image file, ENVI will read the scale factors and apply them automatically, so you shouldn't have to apply the scale factors manually.
Please let us know if this tutorial helped you, or if you have further questions that it did not address. Thanks!