negative signals read from output

thanks for not being helpful at all

Your welcome, thanks for responding so well. When some one comes on and states something impossible is happening and then refuses to believe he is making an error, then a certain amount of micky taking is to be expect. You are making an error or your meter is bust. Do you have the red and black wires connected to the V and Com inputs of the meter. Com = black.

My black lead is touching GND that is coming from my 5V power supply, which is connected to my breadboard.
The red lead is touching the output pins of the arduino, and giving me negative voltages.

So at last you are giving us something to go on, some detail that might reveal what you are doing wrong.
Have you tried measuring the voltage coming from your 5V power supply, by just moving one lead from the arduino output to the 5V power supply output. Is it still negative or has it dropped to zero? Have you tried swapping the red and black wires over, does it now read a positive value.

Where are you connecting the 5V power supply to? Connecting it to the wrong point might give you only a 3.6V logic high output. If it is a regulated 5V it should be connected to the 5V pin NOT the Vin pin. Only use the Vin pin for voltages over 7V, this feeds the regulator that cuts it down to 5V.

A schematic of what you are wiring up would be great.