This seems to be a common issue. http://forums.technicpack.net/threads/block-conflicts-3-1-1.16355/
I have tested this with three different Ubuntu Server 12.04 Configurations, all Vanilla all clean installs of both the server OS and Tekkit server 3.1.1. I Will pastebin my server log this evening, but I suspect it Will be the same as above, It just halts as soon as it hits a conflict.