Sorry that you are seeing this issue. I could not replicate the issue with Sybase DB at my end.
Can you please give us some more information ?
1. Please share MyEclipse Installation Details from MyEclipse > Installation Summary > Installation Details.
2. Also share the Sybase installation details (which Sybase product , the version details and where it is running).
3. Can you please clarify that you can generate entities and see no issues with other databases configured in MyEclipse 2013?