Chris,
I sincerely apologize for the delay in responding, I overlooked the forum notification.
We have been testing our tools with Sybase, it really should work fine. I have a few questions:
1) What OS are you using MyEclipse on, what OS is the DB running on? Does your database use mixed case tables? i.e. Would a table be named “mytable” or intentionally mixed as “MyTable” (quotes used during creation to ensure mixed case)
2) Sybase has a multi level structure, catalogs and then schemas. Do your relationships exist between tables in the same schema? Or do they span multiple schema in the same catalog?
3) Can you try to use the jTDS driver instead of the driver you are currently using? You can get this driver from http://jtds.sourceforge.net/
Though not mentioned on their home page, I belive it should support SQL Anywhere 9.
4) Could you paste the DDL for two related tables (for which you cannot see the foreign keys) here?