Negative numbers in InnoDB Status
I was able to replicate a similar condition by setting the system clock on a server (not Windows) to a time before the time when the MySQL Server process was started.  The numbers in my SHOW ENGINE INNODB STATUS are small since this is a test machine, but they're suddenly negative after changing the clock.

-0.00 inserts/s, -0.00 updates/s, -0.00 deletes/s, -0.01 reads/s


You might try this:

mysql&gt; SHOW STATUS LIKE 'uptime';


This is a value in seconds that appears to be calculated as the difference between the current system time and what the system time was when the server was started... and may be the same number used to calculate these stats.

If you see a massive number (an artifact of unsigned subtraction) that seems completely inconsistent with the server's true uptime then that would be confirmation that this is the cause.

If this is what you find, then I suspect the only remedy is to restart MySQL Server with the system clock set accurately.