For me, PluginManager shows 56 loaded plugins (w/o libraries), but macro "Insert Plugins List.bsh" lists only 31 plugins.
In contrast, an old macro named "Write_Active_Plugins_To_Buffer.bsh" (downloaded from jedit community page, I believe) creates a list containing all my 56 plugins.
jEdit 5.3.0
Oracle Java 1.8.0_73
Windows 8.1
The top of the thing says "List of running plugins", not list of installed plugins.
So technically, it is not a bug. Are you making a feature request of this macro to also list non-running plugins?
I thought, a running plugin is one that's checked on PluginManager's Manage tab. Now, using Activator plugin, I see what You mean ;-)
It's not that important for me. If You find the macro's behavior o.k., then feel free to close the ticket.