Opening a project sometimes gives a blank window on top of the editor window

This one looks pretty similar:
https://youtrack.jetbrains.com/issue/IDEA-270865

Is there anything interesting (like exceptions) in log files, by the chance?

I don't know if my issue is the same; the project loads, I just sometimes get this extra empty window. Sometimes that window won't close using Cmd+W, I have to click the red close button. Sometimes the window pops under the project window and I don't notice it until I switch projects using Cmd+` (since I sometimes need to have multiple projects windows open concurrently).

Sorry, I have no idea how to reproduce it on my side.
It would be nice if you could share the "idea.log" file after the next occurrence, there is a chance that we may find something relevant to the issue there. 

Is there proprietary company or personal info in the idea.log file that could be a liability issue if shared?

There could be some indirect mentions of your personal info like the username part from the profile path, some file names or S/FTP/S server addresses. Thus, I would suggest submitting a support request or a YouTrack report with the attached logs -- both options allow to hide logs from the public exposure.

I noticed empty windows are created when checking out branches using Git Log (which shelves/unshelves file tabs); upon checkout, the window pops up then hides under the editor. If I don't switch to the new empty window and click the red button at the top left (Mac) to close it (it won't close with the normal keyboard shortcut to close a window), then they pile up and come back even after closing PHPStorm and opening it up again, or upon changing projects.

This has got to be a related bug... this caused slowdown on my Mac and the fan to run excessively before I noticed the windows stacked up and closed them all (100+) then invalidated cache.

Unfortunately, I was not able to find anything similar on YouTrack apart from:
https://youtrack.jetbrains.com/issue/IDEA-270665

Would it be possible to submit your own report with the attached log files? (you may set limited visibility for attachments on YouTrack, so only JetBrains employees will be able to see those). Just in case, here is the link:
https://youtrack.jetbrains.com/newIssue

I can try to generate log files etc

I notice the empty windows show up not just 1 per checkout, but many per checkout... it doesn't seem exactly tied to how many file tabs are shelved/unshelved, but maybe it has to do with split view.

Anyway... nobody's able to reproduce this at all?

I also reproduce this. Once I fixed this by doing new project checkout but now (after a few days) it happens again...

Did you notice if there is there any pattern or specific actions that may cause these windows to appear or it happens randomly?

I do not have reproduction steps. If it helps somehow, I am in a period of changing 3 branches constantly...

Looks like, your case is covered by the following ticket:

https://youtrack.jetbrains.com/issue/IDEA-277226

Could you please check if disabling the "Preferences | Version Control | Confirmation > Restore workspace when switching branches option" option helps or not?

Vasiliy Yur

Disabling that feature may stop the problem, or show that it doesn't happen for a while, but it also disables a wanted feature... so it's not a solution. This is like having a squeeky wheel then not driving to see if the wheel doesn't squeek.

The problem also happens sometimes when I open a new project... so never opening a project is not a solution either.

So since we've already got multiple reports of the empty window being generated during branch change and new project open, maybe those features should be investigated, not disabled.

I definitely agree that it is not a solution and not even a workaround. The idea was to test & confirm if this option could be one of the probable root causes.

I have the same problem. Is thee a ticket for it yet?

In fact, IDEA-277266 is a central ticket for this issue now:
https://youtrack.jetbrains.com/issue/IDEA-277226

Please check its relatives as well.