The automatic migration of our project from MyEclipse 2014 to MyEclipse 2017 changed the order of the classpath entries. This resulted in compiler errors after the migration because the order was important. In our case it was an issue with JAXB. At first I thought ME broke something in our project during the migration. But in the end it turned out to have a trivial solution.
I fixed it by manually reordering the items after the migration. Just wanted to let you know in case you want to fix it in the migration wizard.
Sorry that you faced problems with the classpath entries order post migration.It is a known issue with the migration process.Unfortunately the classpath order is pretty hard to maintain with all the different changes during migration and we are doing the best we can do. The migration is a one time process and if you are seeing issues with the order, then please correct the order manually.
Apologies for inconvenience caused. Please let us know if you see any issues.