Yea, we have "A Cristian" holiday yet (began on friday & with monday is to end: Eastern!
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Environment, EMI: I did meen another disturbances, these "field detector" will it not sense, their is only for main frequencies.
I think, that you can have some transients/EMI disturbances in/from your power grid, this can be from a switched high power load/welding or industrial RF generator (plastic molding/microwave sterilizing) etc...
The simplest EMI/EMC check instrument is a old style SW & UHF pocket radio
_ the betetr are very expensive, Field antenna applyed spectrum analyzers & high specialyzed equipments...
But if you have some systems their are good on function; is it inpossible to borrow their card or put your "wrong" one in their good functioning system?
You see, I can believe a bug in sold systems, but you have some functioning cards & some semi functioning, I can not big believe on designer bug in that case... Or is the system on the extremes/limits, that some components are OK, but other can not make the function (enough).
With these oscilloscope resolution is a transient not to check, it can be (only)10-100usec wide, your sampling is slower, but eventual i.e. 20V spike on the +3V3/5V logic supply _the behavioral characteristic is to guess from your system...
Similar problem is if you have short time power missings (drop outs)_ you must the line voltages monitor for some hours over these both (eventual) failure sources: not so very simple to realize-I think.
Sorry, I dont have at the moment some better idea :-(
Good luck in trouble shooting!
K.
Added after 8 minutes:
A newer idea;
If on your board (on some chip) eeproms are: is it possible to erase their "soft info" maybe in a mine searcher equipment at aeroports? (strong X-ray/ high power UltaWideband Microwaves...)
I dont have some experience, but is possible that some cards are others packed for transport & are stressed wild X-rays or "normal" static discharges...
Added after 1 hours 51 minutes:
One more idea: CAN line must be impedance defined; are terminating resistors on the data lines, are the pulses correct/reflection free?