I’m not defending it and the behavior can be annoying, but I hope this is helpful…
There are other detections available (such as the fixlets for “Pending Restart - not triggered by a BES Action” and “Pending Restart - triggered by a BES Action”, at least I thino those are the names).
Bear in mind, BigFix isn’t the product that needs a restart to complete, it is the patch installers that require a reboot, and BigFix can’t really tell whether they’re finished until the installers themselves clear the reboot flags.
A number of products will fail to install at all if there is a pending restart from something else, and I believe they use the same detection logic.
As for checking uptime individually, there is a ‘System Boot Time’ property you might want to add to your column view in the console, that might help.