Sara,
Are you using the ASCOM driver to connect to you Lodestar or the built-in driver "Starlight Xpress SXV"?
If you are using the built-in driver, please update to the
most recent version and rebuild your bad-pixel map. Or, try the SX camera ASCOM driver and see if that makes a difference.
The Lodestar uses an interlaced sensor and software has the option to either read the pixels in two passes (even rows then odd rows), or to vertically bin the pixels and read them all at once. The ASCOM driver uses the former method, and the native driver uses the latter but then "deinterlaces" the data, resampling to produce an image with the same dimensions as if it had not been binned. Until recently the native driver was incorrectly doing dark subtraction and bad-pixel removal *after* deinterlacing. PHD2 v2.4.1i fixes this and does the dark subtraction before deinterlacing. (The dark frames are now the raw, binned pixels thus half the height of the deinterlaced frame.)
If neither of those ideas help, please post a sample image showing the hot pixel (could be a frame taken in the daytime with the camera covered). You can get the sample image by doing File => Save Image. Also please post your phd2 debug log and a zip file of your darks_defects folder. The darks_defects folder is located at C:\Users\YOUR_USERANAME\AppData\Local\phd2\darks_defects
You mentioned setting a SNR value in the brain. Just to clarify, there is no selection in the brain controlling star selection. The only setting in the brain related to SNR is the setting for the Target SNR for Automatic exposure duration.
Andy