I've successfully used BCProgTool with my 396XT directly in Debian, Ubuntu, and Knoppix. Be SURE to read the "readme_first_linux.txt", as you'll need to add a user account for the program, and a few other details. You may need to apt-get ver 8.5 of TCL/TK as well. Most modern systems will already support the FTDI and Prolific serial chipsets, although you may have to manually install those for older distributions possibly.
BCProgTool.tcl TCL/TK Tool
It worked for me, but only after doing the steps in the readme file. I only programmed manually, and never tried the automatic system downloads.