There is an important caveat to using the software to program the Stratalogger: (from the manual)
"Note: You must make the initial connection to the altimeter while the settings are being reported; if you wait until the altimeter goes silent (or is beeping continuity beeps) it will not communicate with the computer."
Of course I did not bother to read the manual carefully and could not figure why the software did not work. And of course I did a Google search instead of reading the manual. Fortunately enough people make the same mistake that I found the answer pretty quickly.
So make sure the software is already up and running, the altimeter is connected, and then turn it one and use the menu Altimeter > Setup right away to change the settings. If you've been able to download the data, you are probably already familiar with this, but just in case.
And, here's a simple trick to speed up boot time at the field: The Stratalogger maddeningly reports zero as ten beeps. So if you set the main for 500 feet, you're in for a long wait at startup. Instead, use 511 feet (or whatever main you want) and you'll save a lot of frustration with your ear next to the rocket at the field. For my BALLS flights, I set the main to 1111 feet, a nice quick four beeps.
Tony