Applying effects increases audio file's length, why?

When I apply one of the effects after the second separator (starting with clip fix) all of the audio files become the same length, which is the length of the longest file. Silence is appended to all of the shorter ones. I wanted to use clip fix on an album, but because of this I can only do it one-by-one. Which is very tedious. Even more so because with multiple windows if one is busy the others are also unresponsive. So I can’t even start multiple at once. (Or use all of the cpu cores)
Why is this? Is it a bug? Or do I have change some setting?

Many of the effects “below the line” in the Effect menu are “Nyquist Plug-ins”.
A limitation of Nyquist Plug-ins is that white space (empty selection) is treated as silence.
“Nyquist” is a programming language that is separate from, but embedded in Audacity. When a Nyquist effect is run, the selection is passed from Audacity to Nyquist, including any white space. Nyquist interprets the start and end time of the selection as the start / end of the sound.

A workaround for this behaviour is to run:
“Edit menu > Clip Boundaries > Detach at Silences” (Alt+Ctrl+J)
on the entire selection after running the Nyquist effect.

Note that this will also turn any other absolute silence to white space. If this happens and you don’t want white space between the audio clips, use:
“Edit menu > Clip Boundaries > Join” (Ctrl+J)
to join the clips back together with silence (this does not add silence to trailing or leading white space).

I would not recommend running multiple instances of Audacity at the same time. Although Audacity should be able to handle this, if you get a crash in one instance of Audacity it will probably trash all of your open projects.

Ok so I either have silence added or removed. Oh well, one-by-one then…

Read my post again.
Processing multiple tracks simultaneously is perfectly do-able.

I didn’t say it wasn’t possible, just that I don’t like the side-effects. Out of curiosity I did exactly what you wrote and got what I expected, the songs became shorter.
Anyway. I worked around the issue by merging the files in foobar. That way I could process it one round and perserve the metadata

If you mean that you mixed down multiple tracks into one, then you can do that in Audacity (Tracks menu > Mix and Render)