I checked this issue on my SDG1005 (FW..27), just to add another model number to the list. I set up my generator and scope as rf-loop did, and I have the same problem with glitches on low frequency square waves on channel 1 only. It only begins to clear up above about 10khz on my unit. Channel 2 is very stable with only a little noise at the bottom of the waveform (no HF oscillations). I set up my scope for infinite persistence and triggered off of channel 2 to show the severe timing jitter between the channels, over 70us peak. About 30 second capture time. Would not want to use dual channel square wave mode for any phase related work! Pulse is definitely better. Oh well. Better to find this stuff out and understand the limitations now, rather than banging your head against the wall trying to figure out a crazy output from a DUT.
Timing jitter is different case. (there you see now channel - channel total. (both channels have just individual random jitter. Also it is good to know that most of manufacturer tell rms jitter. And it is just different case becouse jitter is gaussian random distribution)
Check channels so that look generator CH1 alone. Then look CH2 alone.
Timing jitter is specified: 0.1% of period(typical,1kHz,1Vpp)
And there is not specified lower freq jitter.
50Hz period is 20ms. Jitter (typical) 20us. Jitter from "0" line (ideal time) to positive direction 20us and to negative direction 20us.
It can measure so that trig rising edge. Go to next rising edge and look timing jitter.
(also this is NOT channel to channel jitter)
These glitches is best to look so that trig rising edge and keep peristence on, in this case timing jitter do not overwrite on oscilloscope screen these glitches.
If need less jitter specially with low frequencies it is better to use "Pulse" function and not "Square". Pulse have 8ns p-p jitter independent of pulse freq.
It is not so user friendly becouse if set duty, it do not keep %. All time need adjust duty agen if change freq.
(SDG5000 serie is totally different animal. )
SDG1000 series Square principle: