Lofi,
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.
–Swapna
MyEclipse Support