I am setting the frequency manually, channel 2's frequency setting always follows whatever is in channel 1. Channel 2's other settings, like amplitude and duty cycle will setup independently and do not follow channel 1's setting.

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:
http://www.spooky2.com/forums/viewtopic.php?f=6&t=4324

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