I use the Template forms quite a bit, so this is a pain.
I have one Template that I call “Rough Draft.” I have its tabs set like this:

But when I create a document from that template, the tabs freak out and go to this:

I searched but didn’t see this listed anywhere. I keep forgetting to come over here and post it.
Tab settings are associated with text, not with empty documents, so that’s why your templates are reverting to the default tab settings. There are a few ways to set tabs, depending on where they need to be used.
If you only need them while working in Scrivener (you don’t need them to be used in the Compiled output, or you always compile without having that process modify your formatting), then set them in File->Options->Formatting to make it the default for all new projects and documents created after this point. Alternately, if you only want this setting changed in this project, then use Project->Project Settings->Formatting instead, which will ignore the global formatting settings. If you need it to appear on output that is transformed by the compile process (replacing fonts/paragraph settings, etc…) then you’ll need to customize your compile settings too, so that the output doesn’t mangle your tab stops.
Finally/alternately, you might consider a paragraph style, which you can use import to a custom compile setting, if the tab stops are only needed for specific bits of text that you want formatted differently from the surrounding text.
So, there are two approaches: Global or Project specific default formatting, or a style. Unfortunately, document templates that don’t actually contain any text won’t work for this.