I have a very fast 8 core Ubuntu 10.10 64 bit desktop machine with 16GB of memory running MySQL 5.1.41 but something seems to be wrong with the MySQL installation (even though it's an unmodified stock MySQL installation). I also have a less powerful dual-core Mac Mini running Snow Leopard 10.7 and MySQL 5.0.91.
When loading loading a small 9MB mysqldump generated database the Ubuntu machine takes 33 seconds of wall time and the Mac mini takes 2 seconds:
ubuntu> time mysql --user=root vm-dev -e "source test/database/database.sql" real 0m33.554s user 0m0.220s sys 0m0.030s
macmini> time mysql --user=root vm-dev -e "source test/database/database.sql" real 0m2.077s user 0m0.108s sys 0m0.054s
What kinds of things should I look for that could be wrong with the ubuntu server?
You haven't exactly overwhelmed us with relevant details but considering the huge difference in performance I believe you have a screwed installation. I suggest removing MySQL from the Ubuntu machine, along with any and all related files, rebooting it and reinstalling from scratch.