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Thanks for reporting this. I also see the issue on 4.1.3. Perhaps adding the third party jars under both the Database and Data Modeler preferences will immunize you from it. Of course, this is a bug, and should get logged. It is best if you could do it via MOS since 4.1.3 is a production release. Our team typically only logs bugs for the early adopter releases.
Thanks Gary. Indeed, adding the jars also to the Data Modeler preferences resolves the issue. Nevertleless, I have reported it via MOS, as you suggested
Many thanks again!
UPDATE: After reporting the issue in MOS (yesterday), it has now been logged as Bug 22746791 : THIRD PARTY JDBC DRIVERS DISAPPEARING IF ATTEMPTED TO USE DATA MODELER
Thanks to everyone involved for the swift response!