There may be two separate problems. One, how the makefile flags and environment influence which libraries are linked against. See ld. Second, how the system finds libraries at runtime. See ld.so.
You could have a LD_LIBRARY_PATH environment variable set up in the working environment. But this can be fragile.
The /etc/ld.so.conf could be edited to contain your library directories.
Some old libtool file /usr/lib/*.la could influence your build environment, adding incorrect link options.
When building, you can pass linker flags through the compiler, such as -Wl,-rpath,/path/to/custom/libraries.
In any case, it looks like you are dealing with a mess. How to best clean it up depends on what options you have available as an admin.
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