With this version you have two different helper processes - fetchers and checkers.
Fetcher will only transfer the data from the agents/devices to the checkers to be checked then.
Can you have a look how many of these two helpers are defined in your system?
Rules are → Maximum concurrent Checkmk fetchers/checkers
You can also switch back to the old model with “Use separate fetchers and checkers” turned off.
This can be used to test if there is some difference in the load.
In your case you need more fetchers if they are nearly 100% in usage.