I am pretty sure the problem is warm up related. When the scope starts only external manual trigger works(sometimes) then as time passes it will auto trigger off the external, then manual trigger off the main channels, and finally auto trigger from the main channels(after >20min operation).
I checked pin 3of IC309 and i can see a squre wave whose duty cycle is dependent on the trigger level, only when the scope is triggered, otherwise it is grounded.(My input is a ~1Khz sinewave)
I also checked pin#3 of IC306(NE529) which is labeled trig-IN on the schematic. When the scope starts, i can only see a (heavily) clipped sinewave when external trigger is selected and no signal(+5V) when CH1 trigger is selected. Then as the scope warms up a sinewave will appear there(significally smaller than the external trigger signal). When the sinewave appears, it will manual trigger normally, but not auto trigger. Then after some more time passes it will auto trigger.
Edit: After taking a closer look, it is looking like it is some sort of amplification issue. When the scope is cold, the signal amplitude to Trig.IN (pin #3 on NE539) is small to nonexistent, then as the scope warms up it starts getting bigger. The external trigger works first, because it has a larger signal amplitude, and the auto trigger works last, because i suppose it requiers a bigger signal than the manual trigger.