Actually, it appears to be SOP. Every time I've gone through the line (once or twice a week), the lone TSA agent at the podium alternates between the first/elite/crew/airport employee line and the standard line, whether there is two or twenty people in either one.

The very last time I went through the line, Wednesday evening for my last flight, a new TSA agent was being trained (or at least introduced to how they run things here), and the trainer specifically told her to alternate between the two lines.

Don't know if that's nationwide policy or just how they do things here. Although it can make things annoyingly slow for the elite line, I guess it does seem fair (otherwise, a constant stream of elites would render the regular line completely immobile...).