I upgraded from an svn 3.1 system to 3.2 and had this problem on two sites.
The solution is to go thru and run each command in the file at a time. This is slow but it worked for me as some of the commands in the SQL update file were needed.
Are you running 3.1-2 systems or svn systems?
I hope this helps
tony
Tony Wood : twitter.com/tonywood
Vision with Technology
Experts in eZ Publish consulting & development