I sent the recommendation off to the owner of the server, and we've recompiled everything repeatedly, and still no luck. --with-jpeg-dir=/usr/local didn't work at all.
I've since tried installing and compiling on my YDL machine (which, unfortunately, is sat behind a 56K modem), and it works perfectly. However, doing the same thing on FreeBSD fails horribly.
Furher suggestions would be very much appreciated. Information about the PHP installation running on the server can be found here
Thanks
-Jon