I've already posted this as a reply to one of the posts, but I am making this its own post as well for more visibility.
This is the solution:

1. Import your Presets as always.
2. Apply the broken presets to any random clip.
3. In the effects control panel, select all of the effects from the applied preset + select the OPACITY.
4. Save new preset.

I can confirm this works for both my obsolete transform effects + the garbage matte effects. Previously they both disappeared, but after this work around, they no longer disappear. The reason I chose Opacity is because this setting is generally untouched at 100%, but you can use Motion or Time Remapping if you wish.

Please let me know if this works for you, or if it doesn't work for you.

---Below is the context from which this solution was originally derived---

This issue mainly appears with old presets I've made using the transform effect + new transform effects applied by the extension Excalibur. I believe the primary cause of the presets not being saved is due to them using the obsolete versions of an effect.

Remember how at one point, premiere used to have 2 versions of the "Transform" effect in the effects tab? There was Transform and Transform (obsolete). My guess is that a lot of these broken presets are broken because they utilized the obsolete version of their effects (and for some reason, Excalibur is still drawing upon the obsolete Transform effect).

To prove this theory correct, I imported an old preset that uses a 100% obsolete effect, which is the garbage matte. Importing and implementing it works fine. Upon re-opening premiere, it disappears. Re-saving this as a new preset also disappears, but the workaround with saving a new preset while also selecting opacity, works.

Related Discussion to:

 P: Specific Presets do Not Save when I exit and re... - Adobe Community - 14861962