I just discovered the same problem so, please count my vote too. Selecting a stylesheet in TaskPaper does not appear to stay attached to a TP document. I was just experimenting with replacing my nvAlt document that I use for general note keeping. It is side by side on my screen with my daily TP Task managing page. Naturally I have tweaked the background a bit to separate the two visually. But as the OP said, once I do that, the next time I open my daily task manager TP document, it uses the stylesheet I assigned the other one the last time.
If Jessie isn’t focusing on this until much later then I plan to build in selecting the theme from the window menu using my Keyboard Maestro macro.