When exporting Java source file from VAJ 3.5, the resulting .java files are somewhat jumbled, like multiple lines are merged into one line, etc. What is the problem?

This was a known problem with VAJ 3.5 that caused a lot of headaches. It seemed related somehow to the Source View feature that was added in VAJ 3.5, since similar incorrect formatting can be seen in the Source View.

The good news is that this bug was squashed as of VAJ 3.5.3 and 4.0, so upgrading to either of these newer versions is the best option.