Started the bot with my Chocobo stabled one day, ever since then it will not summon or even show my chocobo as a mount.
You need to unstable your mount. Go interact with it and "fetch" your mount. You can't summon/mount a chocobo you have stabled.
i had this once i played with global settings when i had fall back tick on it was not mounting maybe you have the same
chocobo will only summon if your CR is telling it to. For ultima its just a check box but for kupo you need to change companion from false to true. (I believe for kupo) As far as mount not working when loading new profiles you have to just watch for that. Some profiles and plugin run a scrip/codechunk that usually is labeled "disablemount" so that when they run stealth it doesn't just mount up and break the stealthing. Once the stealth portion is over it will enable mount again. So if you stop one of these profiles or plugins while its in this state then next profile you load will have your mount turned off.