using lot of 100 nf caps is no cure for everything. the location, the kind, brand are all important. Very important is the ESR of the buffer capacitor. Having big caps or an accu does mean zero if they can not delivery a high current very quickly. The Q factor is important. When you have a problem once in a few weeks the cause being software is small (unless you programmed a clock). Software problems are usually easy to repeat.
The problem with the 1284 RX-pin demonstrated hardware can fail in some cases.
It might be an idea to read the reset cause flag and store it in eeprom so you can check it.
Maybe a component can not stand the heat?
And for the PCB : just treat it as if you designed an RF board. Even if it is just an LF board.
Do notice that my remarks are general and specific directed to you, so no need to reply that your board was perfect designed. I believe you :-)
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