Every startup/shutdown process that you can do in the Progress Explorer GUI can be done from the command line. The Agent (Transaction Server) startup command is:
wtbman -i [AGENT NAME] -start
Here is a .cmd file that I invoke as a scheduled process to insure that an Agent is started properly after a WEB server re-boot. My database resides on my WEB server and sometimes the database 'auto-start' is slow enough that the Agent tries to 'auto-start' before the database is up. I invoke this script as a scheduled task at system startup. Note that there is a 'sleep 360' command so that the Agent startup command will run 6 minutes after system startup, giving the database server time to start. If the Agent 'auto-start' has already run successfully, the command-line Agent start will just output a message that the Agent was already running. My Agent is 'GOC-NBSLink', and I am re-directing standard output to a log file.
echo "GOC BROKER START" >> C:\PROGRESS\WRK\import.log
"c:\program files\progress\bin\wtbman" -i GOC-NBSLink -start >> C:\PROGRESS\WRK\
There is of course, a '-stop' option for 'wtbman' if you need to stop the Agent before issuing the '-start'.
Consult the 'Progress Webspeed Installation and Configuraton Guide' for the full syntax of 'wtbman'.