Thanks for reporting this. I understand the error message sounds concerning, the Product team specified that the error is more closely described as "App is listening on port 8080, You could take advantage of an automatic nginx layer available on port 8080 if your application listens on the port defined by the PORT environment variable." for Java runtimes on App Engine. Its unclear how the timer works but it is possible the times is unable to continue counting when a warning is returned and as it sounds like the counter is self coded so if possible can you have it ignore the warning? Otherwise you may be able to exclude the specific warning as detailed by this document <https://cloud.google.com/logging/docs/exclusions#create-filter> if the actual warning log is what is causing the timer to stop as it sounds like the request should work it just also returns an error.
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