Yes, sorry I'll use the right code tags next time (I realised I messed this up just after posting and saw other peoples posts with the proper code tags)
However, I think I've found the root of the problem. This program is a thin wrapper for a shared library. Its built using autotools, and before installing, the executable is not in fact the binary (as you suggest), but is actually a shell script created by libtool which sets up lib dirs and things. I expect this is the problem. I'm not sure yet if there is any way to get around this, my first attempt will be to actually install the program somewhere and run it from there.