Dunno what to tell you...
I just pulled rev 54, and using the console
Code:
create database test;
\u test
source peqdb_rev1751.sql;
source load_player.sql;
source load_bots.sql;
source db_dump.sql;
and it all sourced, no errors. using MySQL ver 5.1.51, 32bit.
Try deleting the database completely and creating it from scratch using the console only. I've had alot of problems in the past sourcing large files with NaviCat.