If we send requests when the IIS server is idle, this may happen. And when the IIS server becomes active, it will response you immediately.
For the problem timeout, I think since the last request can response success without timeout error, it seems IIS server can work as expected. Please check the timeout value which set in client(not timeout in IIS server). If the value of timeout(in your client) is very small, it will lead to timeout error when IIS server is idle(can not response the client immediately).
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