Whenever I connect to HSQLDB from my application deployed on eclipse Juno, it throws an exception as : java.sql.SQLException: error in script file line: 1 Unexpected token UNIQUE, requires COLLATION in statement [SET DATABASE UNIQUE]

You need the latest version of HSQLDB jar, currently 2.2.9.

Your database files are version 2.x, but the jar you are using is probably 1.8.x or earlier. It is important to use the same jar version (major.minor).
http://*.com/questions/12969109/error-in-script-file-line-1-unexpected-token-unique-requires-collation-in-stat

http://*.com/questions/4949023/unexpected-token-unique-requires-collation-in-statement-set-database-unique

2015-04-27T09:22:12.125+0800  WARNING  Script processing failure
org.hsqldb.HsqlException: error in script file line: 234 java.io.EOFException in statement [SET TABLE PUBLIC.C
ONFIGSET INDEX '1 0 1']
        at org.hsqldb.error.Error.error(Unknown Source)

http://blog.csdn.net/YuLimin/article/details/1623656