Had a problem compiling PHP with --with-mssql=/usr/local/freetds , kept saying that it wasn't a valid FreeTDS directory...
Check that when you install FreeTDS from source, that it actually puts the required files from the source directory to where the installation directory was specified, so to fix:
cp [tds source]/include/tds.h /usr/local/freetds/include
cp [tds source]src/tds/.libs/libtds.a /usr/local/freetds/lib
{in this example I installed FreeTDS to /usr/local/freetds}
This may make it a little easier for some else too.