I don't play SWG but I can give you some things to check for. Reset the config/ini file for a clean start, usually a game resolution mismatch can cause a crash. You can rename your profile to save it and start from scratch will fresh ones for your boxes. Utilize the virtual file redirect of IS for this (also in ISBoxer). If you need to, start up the game in a single instance and lower all the settings to min and try to copy/rename that file to be your redirected file.

If you are using 2 monitors try loading your instances onto one screen for testing purpose. To also cover the obvious make sure your game profile points to the .exe for the game and not a launcher app, i.e. station launcher. If SWG has a lot of data to load on startup you can extend the start up delay between instances, the default is 7sec, I use 10 sec with EQ2. I think that is in your team options on isboxer.

To learn about file redirect go to the IS wikia for isboxer and there are links at the bottom for setting up isboxer that explain that.