Since you said you are using the generator in manual mode, ensure that the generator in question is not set to follow out 1 via the sync menu.
You can check this using the generator's menu:
F4 (CH2), F5 (Down), F5 (Down), F3 (SYNC)
You want Trace mode: No
Sounds like it is set to Trace mode: F (Frequency)
Use the F2 - F4 buttons to toggle anything that is shown. T. F (Frequency), T. A (Amplitude), T. D (Duty Cycle)
Then use F1 (Retn), F1 (Up), F1 (Up) F1 (Retn) to exit.
For more details, please check the link:
. Channel 2's other settings, like amplitude and duty cycle will setup independently and do not follow channel 1's setting.