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This error might have been logged when you tried to run the Quick Scan if there were lots of files in the scan path or it was finding lots of threats a the the scan was taking a long time and so was thus unable to finish before your server timed out and killed the process. You might try running the Complete Scan instead of the Quick Scans. Also, you could cross-reference the times in your access_log and error_log files and compare those to see what you were doing on the site at the time of the error.
As the error suggests there is no php process that is allowed to run for more than 60 seconds so that error is not connected with your inability to login for an hour.
My plugin also does not ban you from login in for the span of a hour or any other length of time. I suspect that you have some other security plugin on your site that is causing these other issues.