WJA issues are best dealt with direct by HP. Open up an incident with them and ask for troubleshooting and support first.
If HP is unable to assist you then the next steps are to figure out which one is right, the printer Embedded Web Server/Control Panel or WJA. Chances are WJA is behind and incorrect. The only way the printer would be incorrect is if something impacted the physical memory and page count on the printer. WJA would survive something like that and would need to be reset to the current value of the printer.
I'd put my money on your WJA update process being the problem. Either it is pulling info from the wrong printer and throwing off your reports or it is failing to keep up with the printer in a timely manner.
Run a simple test.
Record the page count on a given printer and its corresponding WJA values
Print off 5 pages
Check both areas again
Confirm if one or the other is properly counting the new jobs.
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