Both are binary-compatible to their respective previous releases and did not have their .so version bumped.
In both libraries several instances of out-of-bounds memory accesses have been fixed. libEBML will also not catch exceptions thrown by an IOCallback instance anymore.
The build system of both libraries has been switched to use autoconf, automake and libtool. Now you can (or have to) use the normal three-point procedure of »configure && make && make install«. The upside is that this should make cross-compilation easier.
In addition both libraries now come with pkg-config files. These are called »libebml« and »libmatroska« respectively (all lower-case). libMatroska's configure script already uses pkg-config for determining libEBML's location. Here the usual environment variables used for pkg-config are used as well (most notably PKG_CONFIG_PATH).
The upcoming release of MKVToolNix will require both of these two new versions.