Maybe clock skew is the wrong word. Basically we'd run the script every 10 seconds, which would use the Jira API to fetch any comments made in the last 10 seconds. So sometimes Jira would return the same comment twice, causing the script to send out two notifications, about 10 seconds apart.
That sounds to me like a Push setup would be preferable here. There are a number of Jira add-ons that can run code in response to system events like a new comment. That way you should be able to avoid the concurrency problems completely.