What the output isn't correct when I use a switching power supply?

I have a circuit that it is a STM32F103RET6(Reference Manual) board and one LCD. everything work very well just one thing! PWM! when I use my J-Link debugger to supply the circuit(or USB connector), the PWM is correct. look:

But when I use my switching supply, the output is:

My switching supply is this and I’m using this module to make 5v from my switching supply. the schematic of my board is this:

Please note that when I use my switching supply, everything work very well except PWM.(I mean even the MCU and LCD work very well). in fact, the problem that I have is just PWM. What’s the problem? how to figure it out?