Haven't run into this before, we tested with pretty much every plugin we could find and it loaded all of them. Are actual plugins missing, or are they scrolled off the bottom of the menu that's larger than the screen height?
Typically, for AE plugins you need to place an actual unregistered copy of the plugin into the combustion Plugins folder, not a shortcut or alias to the AE folder. This is because the plugins must be serialized by combustion with a different number, they don't work properly otherwise. It's possible that some of your plugins are running under the AE serialization, which is why they don't show up in combustion.
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Greg Niles
combustion Product Specialist
Discreet