See page 211 of the manual, the faultfinding section.
https://www.yaskawa.com/delegate/ge...6C&cmd=documents&documentName=SIE-S626-6C.pdf
The second cause is "Failure of the charge current suppression resistor"
The main caps are supposed to charge within the time before the main contactor pull in.
If you manually override that with the caps not charged, you are likely to destroy the rectifier stage due to extreme inrush currents.
There are warnings in the manual that repeated starts will age the charging resistor(s); they are over-run on the basis they can normally cool between starts. On older Yaskawa drives they are listed as a service part but it looks like they now see that as an excuse to charge for a repair...
You mention another relay driver circuit is switching on when you try to start the drive. That will be the initial power on that should start the charge sequence.
Trace the relay contact circuit for the one that is not pulling in - it's either across the charging resistor or controls a larger contactor/relay that has contacts across the charge resistor.
Failing that, look what the relay that is going in applies power to - there may be a small auxiliary rectifier that feeds the charging resistor; that's sometimes used with regenerative PSUs as the main "rectifier" is actually a bank of transistors.
This is Yaskawas resistor notes for one series of drives (I was looking for the spare part for yours but have not found it yet):
https://www.yaskawa.com/delegate/ge...c1-2adf-4737-add7-69542dd0b463/DRV-5WHLKD.pdf
Another manual for a different series, which gives power rating, resistance and part numbers for various "soft charge" resistors for different sizes of drive; see page 54:
https://www.yaskawa.com/delegate/ge...ents&documentName=PP.P5G5.03.Troubleshoot.pdf
It's got one in there somewhere!
edit: The output resistance readings on the MCU are normal. The output stage FETs are off when there is no power but the output is being actively driven low when powered up, so giving a low reading.