Well, that is the issue for sure. I can tell you because I have that issue once and I had to learn it the hard way. Oracle needs that every different product is installed on different HOMES, not only directories but Logical Homes.
For Example, you should have:
1. Home_name1: ORA_DB
Directory: C:\oracle\ora_db
2. Home_name2: ORA_Dev
Directory: C:\oracle\ora_dev
Right, now you're REGEDIT must be mixed and that's why EM is not connecting to your database. What is weird is that your Oracle Developer SQL*Plus is able to connect.
If this is a test database and you really want to do this, you would need to:
1. Uninstall your products. (Using Oracle installer)
2. Make sure to remove the directories you were using.
3. Delete the whole entry for ORACLE on Regedit (LOCAL_MACHINE/SOFTWARE/ORACLE)
4. Re-install both products using different homes.
It's up to you. Let me know if how it goes if you decide to go this way.
Cheers and good luck!