Problem solved here, the make was not indicating the libraries to compile their binaries, I added the following flags to the compiler on the configure options:
LDFLAGS="-L/usr/lib64 -lcuda -L/usr/local/cuda/extras/CUPTI/lib64 -lcupti -L/usr/local/cuda/lib64 -lcudart"
now all the binaries are correctly compiled, even with just the libraries set on LD_LIBRARY_PATH=/usr/local/cuda-5.0/lib64:/usr/local/cuda-5.0/extras/CUPTI/lib64:/opt/tau/x86_64/lib:/opt/mpich2/lib64:$LD_LIBRARY_PATH was not enough.
I have had similar problems when compilating tau, and giving configure the right paths to the libraries, it compiled and installed its components correctly.
Now the hardware events are being correctly registered by papi and shown in tau. These softwares are simply awesome.
Thank you very much for the help anyway.