When you run sps-ctl command with a restart parameter, it is sending a SIGHUP to restart the Apache service. If you use the graceful option, then it sends a SIGUSR1 instead. Therefore, only changes on the Apache configuration will be picked if you use these options.
You can see this if you run the sps-ctl script with the help parameter ("sps-ctl help"), as it will show the differences between all the modes:
[myuser@myserver proxy-engine]# ./sps-ctl help
usage: ./sps-ctl (start|startssl|stop|restart|graceful)
start - start CA Access Gateway Proxy and the CA Access Gateway Engine
startssl - start CA Access Gateway Proxy with SSL enabled and the CA Access Gateway Engine
stop - stop CA Access Gateway Proxy and the CA Access Gateway Engine
restart - restart CA Access Gateway Proxy by sending a SIGHUP or start if not running
graceful - do a graceful restart of CA Access Gateway Proxy by sending a SIGUSR1 or start if not running
help - this screen
Then, to pick the changes done in the Tomcat configuration side, you need to stop and start its service, so the sps-ctl script only can do this with the stop and start options as it uses the proxyserver.sh script to do it.