The Powercommander units basically re-maps the fuel injection software for bikes. It sits between your stock ECU and the injectors.
The Rune runs very lean at low RPM's, correctly in the middle of the powerband and rich on the top end. That's what the baseline results showed when I took the bike to Dynojet. They examine the exhaust gases to see how efficiently the engine is burning fuel.
The Powercommander module can "interrupt" the timing of the fuel injectors to make the bike run properly throughout the entire RPM range. So, at lower RPMs, it can tell the injectors to stay open a little longer to richen the mix, and tell the injectors to close faster at higher RPMs.
It would be kinda like this:
ECU tells injector to stay open for 30ms, but the Powercommander unit gets the message first since it's hooked in-line between the ECU and the injectors. It checks the current RPM's and decides to tell the injector to say open for 40ms instead. The ECU is non the wiser.