I have had this problem before. I have found that when exporting to a .geodatabase, the tables get kind of "crossed" in the process. I tried testing an export in 10.5 and I don't see the issue at the moment. The way I got around it was to edit the configuration tables in the .geodatabase. I believe the issue was in GDB_Items, the Name, Path and Description columns didn't all match, they were crossed. I fixed it by updating that table so that the records all matched for the appropriate table. I wrote a Python script to just alter the rows in the database via SQLite.
My experience was similar to yours in that the FeatureClasses always came out right, but the tables had the wrong schema, seems to only happen when there are multiple tables.
Does that help? I have done a fair bit of digging around in those system tables, so let me know if I can be of more assistance.