Sometimes, the "Next Clip" command is ignored after using the "Amplify" function on a clip

I have “Next Clip” bound to E, if I amplify a clip, then press E, SOMETIMES the first keypress is ignored and I have to send E a second time. I’m trying to automate the process of amplifying a series of clips, and this is preventing it from working. Please help. For some reason, this only appears to happen on my 96,000kHz audio files

It sounds like this bug that I reported Jan 4th 2023: Unreliable macro processing · Issue #4146 · audacity/audacity · GitHub

I’d suggest that you add the details of your use case to the bug report so that the developers are aware that it is still affecting users (requires email registration on GitHub).

A workaround for this bug is to set the Project sample rate in Audio settings to be the same rate as the imported audio file. (You can get to audio settings either via the preferences dialog or the Audio setup button in the main window.)

The problem is caused by the effect slightly changing the time selection if the sample rate of the track is different from the sample rate of the project.
So an alternative work around is to make use of the Store selection and Retrieve selection commands, which are on the Region sub menu of the Selection menu.
So instead of just executing the Amply effect:
Store selection
Amplify
Retrieve selection

If you are creating macros then you could just add these two extra commands.