Thanks to the persistence of user Neurokraft, this issue has been, to make up a word, quasi-resolved

It does have to do with our apps' Preference setting to Launch in background, which is used by some tiny number of users.  To offer this feature, our apps always start up in the background, and then, for the 99.9% of users who have this preference setting OFF, our apps immediately ask macOS to bring me to the foreground.  It turns out that, if there are insufficient system resources, and in particular, if there are more than 75-100 Safari tabs open, macOS will refuse to do this momentarily, which sets up a condition that prevents document windows from opening.

Beginning in version 2.2.17, our apps will detect this refusal, and ask the user to close Safari tabs or otherwise free up system resources.  Although our apps are particularly susceptible as explained above, in my experience, having 75-100 Safari tabs open, for example, makes all apps run slowly.  Therefore our apps are being helpful in pointing this out to the user.

We may take up this issue with Apple someday.

Opening 84 tabs of about:blank will also do the trick. I right-click a folder in Safari's Bookmark Editor containing the duplicate bookmarks and select Open in New Tabs. Weirdness confirmed.

Yeah, I also use Wunderground, though more frequently via the iPhone app or BusyCal integration.

If I wasn't clear, I was using this method to open tabs precisely because it didn't download and render everything, but immediately affected BookMacster just the same. In fact, I've found right-clicking a folder in Safari's Bookmark Editor and selecting Open in New Tabs to be equally effective; I can go from working BookMacster to broken in 40 seconds. This is much quicker than opening the same websites via .webloc files or script. Thought it might be useful in your debugging.

Yeah, no doubt. I ask because, on my computer, Safari can restore (as opposed to initially open) about 100 tabs in just a few seconds, but the effect on BookMacster is the same.

If you quit and reopen Safari, do the restored tabs introduce the same resource burden on your other apps?

Closing a bunch of tabs in Safari cleared up the issue. I had a separate Safari window and when BookMacster stopped opening, I stopped bookmarking and closing, which in retrospect only exacerbated the issue. Once those 84 (!) tabs were closed, I tested opening a lot of windowed applications and BookMacster opened fine. Still, the count from ps -u was only 315. So I brought the saved tab bookmarks over to Chrome and when I opened them there, the issue resurfaced.

At this point I have a practical solution (don’t open a silly number of tabs) but I’m curious if this can be replicated.

Thank you for the tip on Backblaze.   I made myself a note to check it out.

I just opened my /Applications folder and launched a bunch of apps, so that my cmd-tab application switcher showed 62 apps running.  I then relaunched BookMacster a couple times.  Both times, it worked fine.

Here's another idea.  Because there are a few users who like to run BookMacster in the background, BookMacster has this capability, and in order for this to work in macOS, the technique is that the app has a "key" in its package which tells macOS to launch it in the background.  Immediately after launch, it is "transformed" to the foreground.  I just uploaded a special BookMacster 2.2.15-test version which has that key removed.  Please see if that works any better for you.

Thank you for the follow-up, Neurokraft.

One of the users who had the problem before upgrading to 10.12 sent me a list of about a dozen applications, and he said that if any of these applications was running, he had the problem.  This list was a total grab bag, including, I remember, Dictionary.app, which comes with macOS from Apple, clearly not a culprit.

What you describe, that it is the number of programs which are running, and not any program in particular, is consistent with the grab bag reported by this other user, except that you did more testing and figured this out.

But there clearly is some kind of culprit, though, because by the end of the day after a restart I always have typically 25 or more apps running, and I only restart once every week or two to install macOS beta updates from Apple.  Right now my app switcher shows 29 apps running, and this does not include all of my faceless non-Apple daemons – QuicKeys (ancient and unsupported but still works!), Dropbox, BackBlaze, Jettison, NoSleep, etc..  And I have never seen this issue occur.

If what you say about the number of apps is true, then BookMacster should work fine in your Guest account, unless maybe if you launch a bunch of apps first?

Sorry I'm just kind of thinking out loud.  I'm going to have to think about this, and maybe ask around.  What are the approximate numbers of apps/programs, do you think, that causes the problem?