Thanks for the reply Luke.
I removed OpenCV 2.4 in a similar fashion to what you described above ("apt-get remove" followed by "autoremove"), and although this seems to have resolved the conflict relating to my original (non-DIGITS) Caffe installation, I am having problems reading png image files, which previously was no problem within OpenCV 3.
I originally built OpenCV 3 using the following cmake command:
cmake -D BUILD_TIFF=ON -D WITH_CUDA=ON -D CUDA_ARCH_BIN=5.2 -D CMAKE_INSTALL_PREFIX=/usr/local -D BUILD_PNG=OFF -D CMAKE_BUILD_TYPE=RELEASE ..
This prevents OpenCV from building with its own version of libpng (insteading opting for the "system-wide version" of libpng), which has caused me version problems in the past when reading png images.
It appears that DIGITS installation of OpenCV 2.4 is still having an effect with respect to reading png files.
Since removing OpenCV 2.4 and encountering this problem, I uninstalled OpenCV 3 (simply: make uninstall) and then reinstalled it (make clean then make install), however the problem persists. I am confused as to why this is the case.