every time I turn on the scope I quickly hook up to the scopes reference to check
To be honest, I never do that. I touch the tip of the probe with the finger.
About probe calibration. It doesn't need to be adjusted very often, unless really big variations in temperature or air humidity happened since last calibration. About temperature, any calibration has to be done after about half an hour or so of idle running, so the instrument got to a stable temperature/humidity regime. If you calibrate the probe right at startup, after an hour of running, the calibration might be off, particularly if you are in an are with high air humidity and potential condensation.
Another thing, when calibrating, you have to connect both the tip and the Ground of the probe.
In the pic you attached at the OP, there are 2 things:
- a very short spike right after each signal edge - that is from the inductance of the GND alligator wire. In fact, by how tall that spike is, I suspect you are probing with only one wire (as in, another probe was used only to connect its GND alligator to the minus, then the displayed line in the picture is from a second probe with its alligator disconnected)
- then, a long but small amplitude slope, for about half the width where the line was supposed to be flat - that might be from the probe calibration. Not a certitude, but might be.
To eliminate the calibration hypothesis, please post a printscreen of the calibration signal, then a printscreen of the 555 signal. Both taken at about the same time, one after another, and what's most important, both taken by making use of the GND alligator, don't let it disconnected.
A 3rd capture while using the spring connector at the tip of the probe, and by touching the GND and the out pins of the 555 directly with the spring attachment that came with the probes. Then a 4'th pic with the physical circuit on the breadboard, with the measuring probe(s) connected.
I'm asking for all 4 pictures because I know you are careful to details, and particularly interested in getting the optimal. We can discuss the 4 pics later as a concrete example, in order to highlight more details about electronics in general, and probing in particular.