I think I found the problem. Check in the source code to make sure the ADC is turned OFF before entering sleep mode. I added the following line to the TK_OTC derivative of BLF-A6 code, it looks like this:
// Turn off the light
set_output(0,0);
add this ADCSRA &= ~(1<<7); //ADC off
// Power down as many components as possible
set_sleep_mode(SLEEP_MODE_PWR_DOWN);
sleep_mode();
Not sure what code you're using, so it may not look like this.
As far as the current measuring procedure, all we're doing is inserting the low current ammeter into the circuit without breaking the circuit. The series resistance of the low current ammeter is several ohms and won't allow high currents to pass without a large voltage drop. Also typical meters may break the circuit when switching between ranges. But you mentioned Fluke, which model do you have? It may allow you to switch between the mA/A range and the uA range without breaking the circuit, in which case you may not need the jumper, just switch between high and low ranges.
EDIT: read the forth post in this thread: http://www.microchip.com/forums/m525424.aspx
Hope this helps!