I saw the missing info in the post so I figured that could be the issue.
When you say "Same old connection refused errors again on the checks I re-enabled." are you having that error all of the time or is it intermittent still?
If it is intermittent, you may try increasing the timeout to a higher value that what you have and see if that helps. Of if you have access to the host, check it's log to see if there are any clues there.
If it is happening all of the time, run the check in the command line with the -v (Verbose) and post the output here.