STM32F4 custom board design problem
First off: that is a terrible schematic; no ground or power symbols, no logical &quot;flow&quot;, arbitrary boxes for things like the FET... the layout fragment looks good but you should spend some time working on improving your schematics because it takes considerable time to try to decipher them -- both us and you.
Moving on: one thing I notice right away is that your MCU is running off of 3.3V while your sensors are running off of 5V; this is going to cause trouble and it could be taking time for the regulators to finally punk out on thermal cut-off as they &quot;fight&quot; with each other through the sensors and MCU.
You've been asked by several people if anything is getting hot; something should clearly be getting quite warm, and my suspicion is going to be the regulators. A good rule of thumb is that if you can hold your finger/hand on the part, it's under 40C; if you're not particularly heat sensitive the part could be as hot as 50C.
I feel that you are not giving us all of the information. Take your time and methodically work the problem. When the board is cold, the system works. After a while, it stops and you keep mentioning that the rails are shorted. I'm willing to bet that nothing is shorted and the output is simply 0V. Feel around. Something will be getting hot. Probe around; watch the 8V, 5V and 3.3V rails -- something is going to move -- either suddenly or gradually. Put LEDs with appropriate resistors on the 8V, 5V and 3.3V rails -- what do they do, do they suddenly go out, or do they slowly dim?
Like Sherlock Holmes says: &quot;Data, data, data; I cannot make bricks without clay!&quot;