Why would Magento fail to save a customer after generating an ID?
I would add lots of extra logging, try to log it well enough to capture the bug - and to save those logs if the bug can be detected.
Once you have logs that show the bug, you can then isolate the problematic code more easily.
For this, you may need to log the database queries, which might, unfortunately, be tricky if the volume of data is high and/or subject to privacy concerns.