The problem seems to be a little bit more difficult as it looks on first sight.
I have a test-plugin in my user-plugin-folder.
C::B loads it, but cannot load the appropriate zip-file, because immediately after loading the .so-file, all global values in (at least) configmanager are lost.
The plugin is linked a gainst the libcodeblocks.so in /usr/lib (belonging to my regular C::B installation aka nightly).
It seems that loading the plugin also reloads libcodeblocks, but (most likely) the wrong one and therefore loses all the formerly initialised global variables.
Therefore it tries to search the zip-file and all other plugins in wrong folders.
Most likely many other init-values get lost also (I did not check this).
The only way to avoid this, seems to be to remove either the "wrong" plugin, or the libcodeblocks.so in /usr/lib.
The first one makes the plugin unusable for the regular C::B executable, the second makes the whole regular C::B unusable.
I don't see an easy solution at the moment.