Exactly what technique did you use to "connect to it again"? The error message inidicates the method you used may have specified an earlier version of SQL Anywhere.
The following test worked OK for me...
Sybase Central 6.1.0.6424 - SQL Anywhere 12.0.1.3298
-- Create and connect to a datase
Tools - SQL Anywhere 12 - Create Database...
Save the main database file to the following file: c:\temp\data.db
Finish
-- Disconnect from the database
Connections - Disconnect
-- Connect from the database
Connections - Connect with SQL Anywhere 12...
User ID: dba
Password: sql
Action: Start and connect to a databaseon this computer
Database file: c:\temp\data.db
Connect