I built panda from source on my Linux machine using makepanda.py.
I copied the libs to /usr/lib and run ldconfig.
I copied the files in the bin directory to /usr/bin
You shouldn’t have copied the libs and binaries out of the built directory; instead, modify your PATH and your LD_LIBRARY_PATH variables to point to the built results (or cd there yourself).
The makepanda script builds a version of Panda that expects to remain one complete tree; it assumes the config files and Python files will be found in a certain directory relative to where the executable files were found.
If you want to put the tree in a public install directory, you can move the entire built tree to /usr/local/panda (or use the --prefix option to install it there in the first place).
Actually, it is possible to distribute the files around your filesystem, but it has to be done very thoroughly. There’s another post about this very question in the “installation” forum.