since your eclipse files and workspace/s are all run on the
java runtime environment and all configurations are saved at the
file level (no registry edits etc.), it's not uncommon to have
different eclipse versions in different folders running different
sets of plugins, defaulting to different workspaces, etc.
That's the long way of me suggesting a new install in a
different folder and trying it from scratch. If it has the same
behavior, you might try a different version of java.