I have a similar problem in my environment where one of the beacons is showing "Check Connectivity" and all the steps have been followed as described.
However the beacon is seemingly uploading and returning data correctly - so my question is, is data actually being uploaded from the beacon you're having issues with?
Please check the 'C:\ProgramData\Flexera Software\Incoming' sub folders to ensure there are not a bunch of logs waiting to be uploaded.
Check the uploader.log located in c:\windows\temp\managesoft.
I have found the resolution. The servers are configured with a proxy, so i added the proxies into the registry and the beacon is now connected.