The problem is that you are using a MEMS digital accelerometer, and what you are reading is the SCK (serial clock) pin of the serial interface. In order to function, that sensor needs to be interfaced with a microcontroller, that sets it for the sampling frequency, the range and so forth.
So you don't have to expect a square wave with 100Hz frequency, but a fast (depending on the bus bitrate) spike, corresponding to a transmission. Expanding the spike, if the scope is fast enough, you should then see the clock square wave inside the spike.
Moreover, if you don't set the SPI interface correctly, the uC will not generate the clock (the sensor operates in slave mode), and you won't read any value.
If you want to see a 100Hz signal, you could probe the Int pin, which sends an interrupt to the microcontroller every time a measure is available. Then, if you handle the interrupt from the microcontroller properly, you wil see the pulse corresponding to the transmission every 10 ms (100Hz).
But make sure that you're not using motion detection; in that case, only when an acceleration is measured, it will generate the interrupt.
To read the data at the SPI port, the simplest thing is to configure the communication with the sensor; otherwise, it won't send data at all. Then, check if the microcontroller is getting the interrupts and if it's reading the data the sensor gives; you can use a timer to add a timestamp to values and check the frequency they come.
(still WIP)
500kHz is a ways past the maximum specified frequency for square waves for this generator: 100kHz. It appears to have a single-pole RC of about 3.5µs, which would work great for a 0.35/(3.5µs)=100kHz square wave. The output may have a LPF for slew limiting. Also, it is a 50Ω source, so it should be terminated properly to avoid ringing. Try using the TTL and CMOS waveforms, too. B&K have put together this document: Function & Arbitrary Waveform Generator Guidebook .
The external CMOS inverter is not a 50Ω source -- it's source impedance is only a few ohms at most (for low currents) due to VCC and ground impedances and FET RON equivalent resistances. Notice that the output duty cycle isn't 50%, and the edges are ringing.
Best Answer
Well, the oscilloscope should have its own internal function generator for calibration purposes. Usually there will be two exposed pins on the front panel where the probe should be connected. It should be explained in the manual what type of waveform you should expect. This is also important for probe calibration too.
I don't know of any other easy way to calibrate it.
You could always mess with microcontrollers and try to generate some sort of calibration signal, but unless you have another oscilloscope to confirm that the device is producing correct signal, you can't be sure if the oscilloscope or the home made function generator or both are broken.
Another option would be to get it professionally calibrated, but that could be expensive.