Hey guys, I wanted to post what worked for me to fix the issues where Sandbox was cutting off my chat log and/or crashing my windower.
Go to your TEMPS folder inside the FinalFantasyXI Folder (usually playonline/SquareEnix/FinalFantasyXI). Delete everything! Make a folder for each character. Then delete all logs from Windower's log file (usually Windower/Logs) per character. Now, log into each character from the native Playonline Application (Not Windower).
After logging into them you can /shutdown and go back into windower. The logs should now be successfully filtering into the desired character folders instead of mushing together.
Since doing this, I have not had a single swapped chat, expanded window cut off, or crash. I really hope this helps my fellow multi-boxers out there!
~Skye