Not sure what's going on there. One suggestion is to not use `/usr/local` prefix, sooner or later you're going to mess up your system like that (makes you use root and contains other important stuff). Also recommend to use a clean config dir for testing to make sure other settings aren't getting in the way.
Example of building Geany & Geany-Plugins:
```bash
$ export PREFIX=$HOME/local-geany $ cd geany $ mkdir -p ../geany-build $ cd ../geany-build $ ../geany/configure --prefix=$PREFIX $ make install $ cd ../geany-plugins $ mkdir -p ../geany-plugins-build $ cd ../geany-plugins-build $ ../geany-plugins/configure --prefix=$PREFIX --with-geany-libdir=$PREFIX/lib $ make install $ $PREFIX/bin/geany -v -c /tmp/testing ```