Created attachment 159140 [details]
Scripts and screenshot

Hello,

I have detected a problem when using the functionality "File->New" select category "Persistence" and file type "Entity Classes from Database". The creation is classifying incorrectly a 3rd entity as join table and is not created.
I saw bug 77152 to be similar, but it was not reproducible.

I have detected the problem to be the same in Oracle and Mysql databases.
I'm using NetBeans 8.1 but I have tried with older versions and is the same behaviour.
I work on a Mac, OS X El Capitan 

I have created the following example (Mysql commands):

CREATE TABLE TMP1 
(
  ID VARCHAR(3) NOT NULL 
, TMP1 TINYINT NOT NULL 
, NAME VARCHAR(15) NOT NULL 
, PRIMARY KEY (ID, TMP1) 
);

CREATE TABLE TMP2
(
  ID VARCHAR(3) NOT NULL 
, TMP2 TINYINT NOT NULL 
, NAME VARCHAR(15) NOT NULL 
,  PRIMARY KEY (ID, TMP2)
);

CREATE TABLE TMP3
(
  ID VARCHAR(3) NOT NULL 
, TMP1 TINYINT NOT NULL 
, TMP2 TINYINT NOT NULL 
, D1 DATE 
, PRIMARY KEY (ID, TMP1, TMP2)  
, CONSTRAINT FOREIGN KEY (ID, TMP1) REFERENCES TMP1 (ID, TMP1) 
, CONSTRAINT FOREIGN KEY (ID, TMP2) REFERENCES TMP2 (ID, TMP2) 
);

The table TMP3 is referencing TMP1 and TMP2 and adding an additional column.
When you try to use "Entity Classes from Database" you only get TMP1 and TMP2 and TMP3 is marked as join table.

I have figure out that this problem happens only when you have a primary key with two or more columns (@EmbeddedId) in the referencing tables.

Also I find out that if I add and extra column to TMP3, the TMP3 entity is created as expected.

CREATE TABLE TMP3
(
  ID VARCHAR(3) NOT NULL 
, TMP1 TINYINT NOT NULL 
, TMP2 TINYINT NOT NULL 
, D1 DATE 
, D2 DATE
, PRIMARY KEY (ID, TMP1, TMP2)  
, CONSTRAINT FOREIGN KEY (ID, TMP1) REFERENCES TMP1 (ID, TMP1) 
, CONSTRAINT FOREIGN KEY (ID, TMP2) REFERENCES TMP2 (ID, TMP2) 
);

I have attached the script for creating the tables and a screenshot.

Thank you