Please show us the stored procedure that has the primary key violation. Also, show us the application code that calls the procedure and does not detect any exception when the procedure has the primary key violation. The probability that the problem lies somewhere in that code is 0.99999 or thereabouts.

OK, Here's a sample:

The proc:

DROP TABLE IF EXISTS ajs_table
CREATE TABLE "ajs_table" (
  "a" integer not null,
  PRIMARY KEY ("a")
)
insert into ajs_table values(1)  --Insert 1:st row to make exception
DROP PROCEDURE IF EXISTS ajs_proc
go
create PROCEDURE ajs_proc() 
as
begin
  insert into ajs_table values(1) -- Throws exception in ISQL
  select * from ajs_table
end
go
--exec ajs_proc

And the java code:

/**
 * 
 * Project          :   DaVision
 * File                 :   ajs.java
 * First issue  :   2 jun 2014
 * Author               :   janne
 *
 * Notes:
 * 
 * 
 */
package se.whatever;

import java.sql.Driver;
import java.sql.Connection;
import java.sql.DriverManager;
import java.sql.ResultSet;
import java.sql.Statement;
import java.util.Properties;

public class ajs
{

    public static void main(String[] args)
    {
        Driver driverManager = null;

        String _coninfo = "THE_SERVER";
        Properties _props = new Properties();
        _props.put("user", "THE_USER");
        _props.put("password", "THE_PASSWORD");
        _props.put("servicename", "THE_DATABASE");
        _props.put("CANCEL_ALL", "false");
        _props.put("SESSION_TIMEOUT", -1 + "");
        _props.put("CHARSET", "cp1252");
        _props.put("JCONNECT_VERSION", "5");
        _props.put("pbuf","256k");

        // Load the Sybase Driver
        try
        {
            try
            {
                Class.forName("com.sybase.jdbc3.jdbc.SybDriver").newInstance();
            }
            catch (Exception e)
            {
                Class.forName("com.sybase.jdbc2.jdbc.SybDriver").newInstance();
            }
            StringBuffer temp = new StringBuffer();
            // Use the Sybase jConnect driver...
            temp.append("jdbc:sybase:Tds:");
            // to connect to the supplied machine name...
            temp.append(_coninfo);
            // on the default port number for ASA...
            temp.append(":" + 2638);

            if (driverManager == null)
                driverManager = DriverManager.getDriver(temp.toString());
            Connection conn = null;
            // Create Connections
            conn = DriverManager.getConnection(temp.toString(), _props);


            Statement stmt = conn.createStatement();
            String sqlStr = "exec ajs_proc()";
            ResultSet res = stmt.executeQuery(sqlStr);
            while (res.next()) 
            {
                System.out.println(res.getInt(1));
            }

    }
    catch (Exception e)
    {
// We do not get to this poin as long as proc. ends with select
        System.out.println(e);
    }
    }
}