I would try to remove the bootloader first and test whether the project now runs. Probably the bootloader is waiting for an event that does not happen.
Chip won't miss power on reset during power up, you may try to use LED indicator or output IO to debug the code execution status difference between power up and manually reset.
What do you mean the chip won't miss power during power up?
There is only 1 source of power to the board and everything "dies" when this power isn't connected.
When I apply this power to the input, I see that all voltages are OK (5V) and also measure 5V on XRES pin of the MCU.
According to the application note, the MCU should have kept the reset pin at 0V during power up until normal operation and then release it to be pulled up by the internal resistor.
VisionZ is suggesting to use a simple LED, connected to GPIO, as an indicator to aid in debugging the issue.
The document you reference (AN73617) is not for PSoC 4 devices. Have a look at AN73854, AN68272, AN86526.
Question: is the project configured to be bootloadable?
AN73854 describes how to configure the project to be bootloadable.
Question: did you put a bootloadable component in the schematic?
Chip won't miss power on reset during power up
The project is indeed configured to be boot-loadable and I put a bootloadble component in the design.
Sounds like you have the right approach for a bootloadable design. Maybe a bit more detail would help us, if you don't mind.
Are you using a Cypress KIT? If yes, which one?
If this is a custom hardware design, which PSoC 4 device are you using? BTW, PSoC's do not have a bootloader installed when they leave the factory, unless they are part of a Cypress KIT. A bootloader can be installed in a blank PSoC4 using either KitProg or MiniProg3.
When manually reset through programmer, are you using KitProg or MiniProg3?
Does this design use Power-On Reset, or XRES, to reset PSoc 4?
Is the bootloader a custom design or the one provided by Cypress?
Did you Build the bootloader and point to its .hex, .elf, generated files with Creator? If these files are not pointed to by the application project/workspace properly, then it won't be loaded into PSoC4 when PSoC4 is being programmed.
Have you tried a simple bootloadable Blink an LED project, using Cypress project + Bootloadable component?