Thanks for looking into this, ChrisR. Sorry to take up more of your time (I think you deserve a quiet weekend after the great new projects last friday).
Thanks for confirming that this is "just" a timing issue. I will try your suggestions when I make new test builds. But for now, I decided to fiddle around with "x:\windows\system32WinT.exe" myself, in my autohotkey.ahk (autorun) script, as it is a timing issue, and autohotkey runs pretty late in the process as well (I use it for mounting my iso with portable stuff, some extra fonts, and of course hotkeys).
Playing around with different timings in autohotkey.ahk is just easier for now (no need for new builds).
The best result until now is: run wint.exe, wait 300 milliseconds, run wint.exe again. Now I always have the taskbar (tested on 3 different systems).
I compared the new 20150912 Win8.1SE project with the 20150325 version, and to my surprise I saw there was not any change in the build\9-AutorunCfg.Script at all, so I don't know why the timing issue has cropped up again. As I said, I tested on several systems.
So for now, I will maybe keep the Autohotkey.ahk solution, at least until we hear if others are having trouble with the taskbar appearing. Or maybe everybody's on Win10PESE?

My favorite is still Win8PESE64, it just works every time, 7PESE and 8.1SE just have these little timing issues from time to time. Pretty strange, Windows 8 is my least favorite desktop OS, but I like it for making a PE from it. Like in Monty Python's "Holy Grail": Windows 8 is the Witch, 8PESE is the bridge ("build a bridge out of her!"). Sorry, I digress...
https://www.youtube.com/watch?v=zrzMhU_4m-g