Ok, so this is interesting! I ordered some new 5MHz resonators. Thought I might as well have a poke around to see if I could find anything and...nope.
Then I was looking at the resonator under the microscope and thought I saw a hairline crack, so got the tweezers out and started to poke at it gently. Soon realised it was just residue of the conformal coating, most was removed in the cleaning bath.
Now that I had scraped it my OCD said "got to remove it all from that resonator" while I was scraping it (pretty gently, not rough), the entire metal top of the resonator came off and I was just a thinking..."ok, that wasn't meant to happen". Due to the ease of how it came off it probably wasn't in a good state to begin with.
Anyway, once the cover was off I could see the ceramic resonator and again, under the microscope I thought I saw a crack, so thinking "might as well, got new ones on the way", I poked at what I thought was a crack, but it was just a residue and half the ceramic was covered in this white residue. So very carefully I removed it with the tweezers, just scraping away. Once I was done I though "lets power it up".
I couldn't believe it! It actually turned on, no loading with a scope probe or anything! It did the full needle sweep and boot up sequence. So something is definitely not right with that resonator....even before I removed the cap for it. Glad I have some more coming, hopefully tomorrow.
I now have 1 unresolved issue.... The M66242 (datasheet here...
http://pdf.datasheetcatalog.com/datasheet/MitsubishiElectricCorporation/mXyzuwuy.pdf)....so the voltage to the external ceramic resonator for this IC is about 600mV which clearly is not right. The IC has power and all 4 of it's PWM outputs are held high at 5V. So...why is the resonator voltage so low. Could a bad resonator be pulling it low or is it likely something to do with the IC itself?
EDIT: Decided to give the resonator for the M66242 a poke also and it's cap basically fell off! I wondered if it was me being a bit rough so I grabbed one of my projects which uses these same resonators (pic below) and I put more effort into it than I did with the ones on this board, but it held firm. I obviously didn't go too far as I don't want to break it, but it definitely held up better than the 2 that came off!
Oh, and turns out the "white residue" on the ceramic is normal, this other one has it too, but looks like its a lot cleaner. The other one may have had some liquid get in as it looked a little "washed out" for lack a a better term in comparison.