Sreg,
First, just to be sure we're on the same wavelength, short pins 1 and 2 on CN1 (on szmeu's schematic) together and put the device-under-test (DUT) between these shorted pins and ground. For now, just ignore the possibility for a four-wire setup (actually three wire with the circuit from szmeu).
OK, you've done that. Now, with a 30mV pulse across your DUT, you can do the math and you should have approx. 600milliOhms +/- for the DUT. This assumes that at top of the 100 Ohm resistor, R8, (where it connects to the emitter of Q1) you see a 5V pulse.
If that's the case, then you may want to make sure that the oversampling is set up correctly for your device. You may need to change some of the register set stuff in the original code. This stuff...
sbi(ADCSRA,ADPS2);
cbi(ADCSRA,ADPS1);
sbi(ADCSRA,ADPS0);
Refer to the datasheet for your device and the Atmel document that szmeu mentions.
Then again, it could be something simple like the discharge transistor, Q2, is always on. Or you didn't change the value of Vref in the code. You mention the internal ref on your device is 2.56V. In the code it's 1.1.
This is all just guesses on my part. Maybe you have checked all this stuff. My 2 (euro) cents worth, anyway.
Good luck!
- Totoro