Please, don't put too much effort into it on my account, as it is a minor (non-fatal) issue, as I indicated above. It's probably only me that has experienced this minor problem, because I tend to push apps a bit more than most (which can sometimes be useful in Beta testing).
I invoke DCU directly via a button in FARR, rather than tell FARR to run an update check. That way, I get DCU to scan all apps (as per the screenshots in an earlier comment posted above) and report on the currency of all installed versions of those apps versus the latest version on the DC website.
I figured that it was, as you describe above, "...likely that it's related to the DcUpdater functionality that purposely only shows certain items if it's invoked and told to explicitly only scan a certain folder.".
I was aware that it would happen, as you say, if I did "...an update check FOR/FROM A SPECIFIC PROGRAM.".
What happened was I read the threads about DCU and SC being given new updated versions, and so I then triggered DCU via the button in FARR (1st time). This gave the report of all apps, with DCU and SC highlighted as having updates available. I then started the update for those two, and the updates installed OK.
I then triggered DCU via the button in FARR again (2nd time), and just the two apps - SCU and SC were reported on. I checked the paths in the two relevant .dcupdateredirect files to see if they had been changed (they hadn't).
I then shut down FARR, restarted it, and then triggered DCU via the button in FARR again (3rd time) and DCU provided the expected and correct full report of all apps, including the two (DCU and SC) that had just been updated.
So yes, it does seem that, as you say, "...what's happening to you is that on your second call it is maybe restricting itself to items in a specific folder.".
When I re-ran DCU (2nd time and 3rd time), I did not think to check whether DcUpdater was already running in the systray - I suspect that it must have been on the 2nd time. I would have made more careful a note of what occurred at each step, had I not been in a "workaround" frame of mind and had I been expecting to tell you about the problem. Telling you about the problem was just an afterthought - it was a belated "I should probably report this to mouser" thought. I shall try to remember to take more careful note of each step at when I run any new updates after this point.