What do you mean with:
I also go into the table and change the NOT FOR REPLICATION value to NO.
I don't think you can do that. That is, I don't think you can use ALTER TABLE to remote NOT FOR REPLICATION. Instead you have to create a new table and copy data over.
Now, you are using a language like a table was some sort of GUI object with checkboxes, but it isn't. There is the Table Designer in SSMS which may make you think it is, but this is a dangerous tool. It can implement the rename-create-new-and-copy-over dance for you, but it is 1) very buggy 2) it may use it, even when ALTER TABLE would do the job. If you use it, always get the script and review the script carefully. They do some things very wrong there.
Anyway, on which instance did you make this change? Publisher or subscriber?