Thanks folks for all your help. I have it working now again. Somehow I must have made my system believe that it was a folder. I think when I tried to view the content of the package (thought is was a script), I opened it up in TextEdit. That must have screwed it up.
If someone stumbles across the same problem one day, here is how I have fixed it.
1) I got the app "File Matey". http://www.macupdate.com/app/mac/25470/file-matey
2) With it, I viewed one of the offending plugins.
3) I checked "has bundle bit".
4) Saved the plugin.
Now it doesn't look like a folder anymore. Now you can right click on it and see that it was assigned to be open with TextEdit.
I changed this to Animation:Master and check that all files with the same hxt extension will be changed.
Voila, A:M recognizes the plugins again.