It waits until some of these 1000 threads finish execution.Since the host monitor or the RCC is still responding, one must assume that the monitoring task is waiting, but for what?
Do you see some "Timed out" or "Checking" test items?
You are right, our mistakeIncidentally, there is in the UDP test method a small bug. In the GUI I enter 2 seconds for timeout. The variable AlertThreshold but shows 2 ms

Will be fixed in next version.
How many URL test do you have?At URL checks often the Windows timeout is registered.
I think we don't need just messages about pause. We need list of tests that take too much time for execution.What we need in my opinion is a more detailed debug logging: Perhaps it is possible to generate messages in syslog when within a minute no more tests were performed. If appear in the log a list of current tests, one could limit the error might easily.
And probably you already have such log. "Timed out" items should be recorded into regular log that stores test results. Do you see such items?
Its more difficult to catch tests that take 3 or 5 min for execution.
You can adjust one internal parameter and tell HostMonitor to mark test as "timed out" after 3 or 5 min (instead of 15 min by default) but then some "normal" tests that need a lot of time for execution will fail...
When problem appears, could you check for "Timed out" test items (Unknown status, "Timed out" reply string)?
Test items that stay in "Checking" status for a while?
Do you see "timed out" items in the log?
Regards
Alex