The photos are trully amazing!
Nice laser too! ;)
But i fear your driver is out of regulation. Did you use one of Rkcstr's drivers?
The PHR diode at 100mA needs around 5.3V or so. The driver itself needs 2.3V more than that, to keep the current constant. So the minimum voltage required for regulation is ~7.6V. That is above the nominal voltage of two Li-Ions (7.2V). When they are full, they have 4.2V each, so freshly charged they give you 8.4V, or ~8V under load. You then only get to use a tiny part of their capacity - by the time the voltage drops by 0.4V, the current and with it the power start dropping.
If you use two 3V batteries, the driver can't regulate at all, so the diode never gets the required voltage for 100mA to flow, which is why it's dim from primaries....