Try running 'export' and see what PATH says.
Then, assuming it has worked okay, you need to look at which path the shell script is trying to put on the front. For my toolchain I set various env vars:
CC=arm-linux-gcc
CXX=arm-linux-g++
CCX=arm-linux-gcc
CXXX=arm-linux-g++
COMPILER=arm-linux-gcc
LINKER=arm-linux-g++
G77=arm-linux-g77
F77=arm-linux-g77
PATH=/usr/local/arm/3.3.2/bin:/usr/local/arm/3.3.2/arm-linux/bin:$PATH
Now I've also added /usr/local/arm/3.3.2/arm-linux/bin which contains (for example) a file called gcc which is linked to ../../bin/arm-linux-gcc and the same for the rest. This means that even if the compiler just tries to call gcc, it'll get the cross toolchain version.
It looks like your script only adds the one containing the commands with prefixes (like arm-linux-gcc, etc.) to the path, this means that when make tries to call gcc, it'll get your default version.
Therefore, either edit the script to add the extra bin directory, or set the CC, CXX, etc. env vars in the script (and they will/should be picked up in the configure and Makefile scripts).
Regards,
Simon