Hi bankaienator
I looked again at the photo you posted, and found the manual for the Agilent 33210A you are using:
The indication on the Agilent display is that your waveform is alternating about a 0V DC offset, which is the default for the Agilent.
Check out pages 20 and 21 of the manual for how to set the signal limits to 0V and +5V, and see if that helps.
Also, for testing, it looks like the square wave output from the Agilent can have its duty cycle varied easily. This might be a good place to start.
All the best
Ray