Dear Naoum,
Thank you for your helps:
1. We are using our Own design
2. I checked the power sequence, and saw that the USB_V0 has the only 10 micro second after the 5 Volt is applied, while the 1.1V Vdd has 100 microsecond delay. There was a load switch between external 5 Volts to USB_V0, which was controlled by BCTRL signal. But it was not working, so I removed it, but I could not see any improvement.
3. blue line is for XTAL. I noticed that the voltage level (600 mVolt) is below then the requirement (Vdd*0.75= 825 mVolt), and re-measured the voltages with another calibrated oscilloscope as 850 mVolts and 888 mVolts. So the voltage levels are in the acceptable range. I am not using the exact crystal in the reference design, instead, I am using NX3225SA-24.000000MHZ which was for i.mx258 ref. design
4. If it does not stop the processor reset/boot, I don't care the slow start-up at the moment, but I also added 1 MOhms, but could not bootloader to start.
6. I have an UART/RS232 chip (ADM3101E) for UART_0, and set the BOOT_MODE_1=0 and BOOT_MODE_0=1 for serial bootload, and RCON21=RCON20=0 for UART_0. I am using PTB10,PTB11 pins for UART_0. I saw 0x23454523 pattern is coming to the RX pin, but nothing is in TX pin. I am not using RTS and CTS pins of UART_0, I wonder if bootloader needs them? I am using same 74LC541 chips for bootloader config pins, and checked that the config pins status are applied to the processor during 1 miliseconds reset.

Best regards.
Mehmet Ali