It sounds to me as if your MDB file contains both your code and your tables. When you create the MDE file, it will contain copies of everything--both the compiled code and the tables (though not the source code). When the code in the MDE executes, it processes the tables in the MDE. This is what it is supposed to do.
What you expected it to do, I assume, is process the tables in the MDB file. It won't, because code and macros are only aware of tables in their own database. (Actually, code can process tables in another database, but that's not the normal way of doing things.)
If I'm right, what you need to do first is run the Database Splitter on the MDB file. That will move all the tables to a new database, and replace them in the MDB file with "linked tables" (surrogates for the tables in the other database). After that, the code in the MDB file will make requests against the "linked tables", and the Jet engine will execute the requests against the tables in the other database.
Once that's working, you can create your MDE file. The MDE and the new database that contains the tables constitute the application; the original MDB database you keep for yourself, so you can make changes as needed.
Is that what you needed? Rick Sprague