Your circuit is basically this:

When you turn on the transistor, it basically shorts out the battery. I bet your batteries are nearly dead, and I bet that if you measure the battery voltage when the transistor is on, it's about 2.52V, not 3V. Why? because you measured the base current at 1.32mA. By Ohm's law, 1.32mA through a \$1k\Omega\$ resistor means the voltage across the resistor must be \$1.32mA\cdot 1k\Omega = 1.32V\$. The two base-emitter junctions of T1 add another 1.2V: \$1.32V + 1.2V = 2.52V\$
R1 and R2 represent the internal resistance of the batteries. I've used \$200m\Omega\$ here, which is an estimate for a fresh battery. As the batteries deplete their stored chemical energy, this resistance becomes greater. The consequence is that when they must pump more current, their voltage decreases more.
It's a bit odd that you are measuring more collector current than emitter current. I bet you measured the collector current first, and by the time you measured the emitter current, the batteries were more dead, and this is why you measured less emitter current.
On a practical note, the current gain (\$h_{fe}\$) of transistors varies, a lot. Even two transistors of the same model can have very different current gains. A well designed circuit should thus be relatively insensitive to this parameter. If you wanted to make 1A flow through the transistor, you should not try to find the right base current to make that happen, but rather limit the current through some other means, then calculate the necessary base current, then give it a bit more base current to be sure the transistor is "saturated", that is, as "on" as it can be. Thus the voltage between the collector and the emitter of the transistor will be at its minimum.
Here's a more reasonable circuit for experimenting with transistors:

Here you see the collector current is limited by R4. Of course, you could power an LED directly from your microcontroller. A transistor like this becomes more useful when your load is big enough that you can't do that. Imagine it's a headlight, instead of an LED.