That is very weird. I have no problem replacing any of them with my rotary slider effect.
I also tried removing all plugins and adding a Cabbage3 one to the top of the list, no issues there either. I wonder why this is happening. It seems that if you can add them further down the list, you should be able to add them anywhere 
Trying to replace the Noise Gate:
Trying to replace Pedalboard:
Removed Noise Gate and trying to replace Pedalboard:
Removed all plug-ins and trying to add:
What success looks like (adding Rotary Slider “ROTA” to the second slot when the first slot is loaded with something else):
Really weird, right?
I don’t really understand, The plugins are listed, but when you hover over them they don’t get highlighted? Is that it? because from the picture it looks like you just need to move the mouse over the plugin name to select the plugin you want. But I assume you’ve already don’t that. Can you run auval -a from the command line and post the output?
Sorry that was confusing. In the first picture there are five Cabbage 2 plugins. In the second picture there are eight Cabbage plugins (the first 5 and then 3 new ones that are all from Cabbage 3). Those three (GateLoopCab3, KEYB, and ROTA) are the ones that are the issue. In the third and fourth picture it is back to the original 5.
And those three are synths? They can’t be added to an effect slot, but they shouldn’t be missed there. Have you tried closing MS and running those commands I shared earlier? Your cache might be messed up.
Yes, I’ve run all the cache clearing commands.
This is one effect and two synths. All three work as intended … as long as they are not in the first effect slot. If I try to load in the first slot then none of the three appear in the menu.
Here is the simplest example I can think of:
<Cabbage>[
{"type":"form","caption":"Effect","size":{"width":580,"height":300},"pluginId":"GAIN"},
{"type":"rotarySlider","channel":"gain","bounds":{"left":500,"top":200,"width":80,"height":80}, "text":"Gain", "range":{"min":0,"max":1,"defaultValue":0.5,"skew":1,"increment":0.01}}
]</Cabbage>
<CsoundSynthesizer>
<CsOptions>
-n -d
</CsOptions>e
<CsInstruments>
; Initialize the global variables.
ksmps = 32
nchnls = 2
0dbfs = 1
instr 1
a1 inch 1
kGain cabbageGetValue "gain"
outs a1*kGain, a1*kGain
endin
</CsInstruments>
<CsScore>
;causes Csound to run for about 7000 years...
i1 0 z
</CsScore>
</CsoundSynthesizer>
It works in MainStage, but only when it is second or later in the effects chain. It does not show up in the list if I try to load it first.
Here it is working (loaded in the second slot):
And here is the Cabbage list for the first plug-in slot:
Really strange.
I think I can now replicate this here. I’m not getting the exact same behaviour, but it’s odd all the same. For some reason now, when i try to load a plugin in the first slot, no CabbageAudio plugins show for me in the list. I don’t get it, I was able to do this yesterday without any issues
p.s. I"m travelling for much of today, so I owno’t get a chance to delve further into this until tomorrow. It’s a head scratcher 
I’ll try with different numbers of input/output channels to see if that is the culprit. My intuition is that there’s something unique about the requirements of the first plugin matching the track.
Is there anything from the auval test that would help understand?
Not that I can see. It looks like all of the tests pass.
I don’t understand why it worked fine for me yesterday but not today. Also, I think it would be strange if the first slot of an effect track needs to be different in terms of plugin types than the rest. When you scan the plugins, does noise-gate show as something other than an aufx?
Have you tried this in Logic? I’m not seeing the same issue in GarageBand as MainStage. There it seems I can add the Cabbage plugin anywhere I like
None of my Cabbage 3 plugins appear on tracks in Logic.
I see them in the plug-in manager in Logic. But doing the report on the plug-in (I forget what that is called) does not produce the same scan as MainStage.
I ended up purchasing Logic in order to get to the bottom of this. I see the exact same behaviour in Logic as I do in MainStage 
I can add a Cabbage3 plugin on some tracks, but not others See the video below.
All we have to do is change the input to stereo 
I can’t believe that was the problem!
However, we should still be able to configure the plugin to support both mono AND stereo tracks. I’ll take a look into this now.
Bizarre.
When I do “reset and rescan selection” on my cabbage 3 plug-ins in Logic, this is what I get:
Fetching Audio Unit info for gain
Done
In MainStage I get the full Audio Unit Validation result. That is part of the reason why I was so focused on getting it working in MainStage.
But the good news is that Cabbage 3 plugins do appear in Logic as available if tracks are stereo.
If you set "channelConfig":"1-1", i.e.,
{"type": "form", "caption": "", "size": {"width": 580.0, "height": 500.0}, "pluginId": "def3", "enableDevTools":true, "channelConfig":"1-1"}
they’ll show up on Mono tracks, and can be loaded to stereo tracks as dual mono. I need to look into how to support both mono and stereo, but at least we’re up and running now. 
Great! Pretty much every plugin I write is mono->stereo since I’m usually processing a guitar, microphone, or mono synth.