Arduino UNO: How to connect 2 way power for DC Motor?
On the Arduino, the 5V supply is the same as the 12V supply EXCEPT it it shunted through the SMT 5V regulator.  This 5V regulator is powering nearly everything on board (when USB isn't hooked up), and running a motor on it is a bad idea:


Motor voltage transients are placed directly on the same voltage as your microcontroller - brown-outs are the least of your potential issues.
The regulator is protecting itself by dropping the voltage and - thus - the current.  You are likely hitting the internal current limit of the regulator.  You need to provide your own regulator if you want to drive the 5V motor.


Better solution: You could also PWM the 12V down to 5V.  For motors, PWM works very well for 'voltage scaling'.  In other words, if you run your 5V motor on 12V and PWM to 42% duty cycle, you have the equivalent of a 5V supply.  Your chip has a PWM input, just use that and power both motors from the 12V supply.

Have fun!