Good question. In both PAC Control and OptoControl (config mode), if you've selected: Configure > Full Debug from the menu up there at the top, you'll get a bunch of extra stuff (those line numbers you saw) compiled into your strategy. This allows you to step INTO individual blocks when you're in debug mode. Might also make sorting through strategy files a little easier.
The trade-off is that, when you've configured/compiled for Full Debug, you now have all that extra stuff which makes your strategy run a little slower overall. So when people are really trying to squeeze every possible CPU cycle out of their controller for some time-critical process, turning off Full Debug shaves a little time.
You might also be interested in this post where I talk about that LINE.NUM and backing up files, etc.