It appears to be a problem with (shock, horror) this lead-free ROHS compliant solder that's used. These older boards, especially Pentium 4s, got really hot. Add a day to day duty cycle of cooling at night and heating up during the day, the solder just cracks. Reflowing either the specific chip or the whole board appears to be the only real, long term method of fixing things.
Since posting this, I've had to reflow another 5 boards to stop this behaviour. It's only a specific model that needs this doing so far, but it's annoying nonetheless. For that X58 board getting the same issue, I think it would have to be a south-bridge issue, since Super I/O chips are rarely used now. In that case, you'd need some specialist kit to handle that kind of job, ( an IR board pre-heater, hot-air gun with a wide area nozzle and mount). You could just bung the whole board in an oven (like people do with graphics cards) and hope for the best, but it ain't exactly a healthy method.
It's funny really, the volume of weird and quirky issues I've come across, fixing these PCs. We go through bins full of hard drives, since we have a very low tolerance on failure, being a single remapped sector under test. I've personally come across dozens of computers that fail to boot, simply because of bad RAM. Power supplies are the bane of nearly every PC I come across - to which I've exploded 4 so far. I'll tell you now, when a varistor pops, you giggle, when a filter cap blows, you're startled, when a 450v 100uF mains input cap blows... you fucking shit yourself (they're the size of a D cell battery).
You'll be surprised to know and just how many issues resetting and shorting out the RTC CMOS and BIOS can fix. Disconnect from the mains and allow the system to discharge fully, remove the battery, remove the jumper, short out the two battery contacts and press/hold the reset button (if it has one) for 5 seconds. Put the battery back in and turn the system back on. Often, I power the system back on with the jumper still removed (though some systems fail to boot if you do). Jump into the bios when prompted and then put the jumper back in. Load defaults, save and reboot. This can fix a wide variety of issues, like mismatched memory, failed bios updates (if the system can not update at all, not if a bios updates but fails as a result), system won't POST, random MB issues, COMS problems with serial... it's a fairly standard cure-all really.
I've heard PCs that sound like car engines, humming away due to an imbalanced fan. I've had a power spike rev up one of those blower-type fans (hamster wheels), and break some of the fins off.
Fixing a bent pin on a 478 is tricky, but on an LGA775, it's brutal.
When it comes to cleaning... ye gods... Let's just say that I fully support Apple's warranty failure on a smokers PC.
Anyway, there is one issue that has me somewhat baffled. Integrated Network Interface Cards (NICs) that 'forget' their MAC address. Work that one out peeps. We get so many motherboards in that have no MAC address, it's not even funny. Trying to fix them though, is extremely difficult, since we don't know where the issue originates from. Often, the MAC is stored in the EEPROM next to the NIC, so reflashing the EEPROM can technically fix it... but how is it happening in the first place. If the MAC is built into the NIC chip directly, well... you kind of need a new chip, which is pretty much impossible, so you replace the whole motherboard.
SoCs are going to be the bane of modern computers. If something goes wrong... you need a whole new unit. Disposable electronics at it's best, I guess.
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