After searching for a while I found the solution in a couple of blogs, so thanks to
Pablo and Shimi. These contain a more detailed background if you're interested.
The problem related to something called the Agent Controller being linked to an old version of libstdc++. To solve it you can run the following two commands:
wget mirrors.kernel.org/ubuntu/pool/universe/g/gcc-2.95/libstdc++2.10-glibc2.2_2.95.4-24_i386.deb
sudo dpkg --install libstdc++2.10-glibc2.2_2.95.4-24_i386.deb
Though your mileage may vary depending on distro version etc.
You should then be able to profile successfully in Eclipse, I found that I didn't even need to restart Eclipse.