I'm trying to reproduce this, and these are the steps I'm currently following, which are not reproducing the issue you describe:
1) Log out
2) Log in to ACP
3) Click Appearance > Styles
4) Click on Style Properties for a style that has no customized components (style 'bla')
5) Edit and save a style property (I was using one of the palette colours)
6) Click on Search templates in the sidebar
... style 'bla' is selected in the style drop-down of the search templates form
Would you be able to identify exactly what you did to see this behaviour?
I'm getting some pretty inconsistent results while trying to reproduce it, like when I first logged into the ACP I was able to reproduce it just using my steps in the 2nd post. Then I went to another site on the same server running the same version (beta 2) and couldn't reproduce it.
Following that I returned to the first site where I could reproduce it but I am no longer able to. So I then tried this while viewing (in the ACP) my custom style:
Went to the style list
Selected style properties on the default style (went correctly to the "default style" properties)
Did nothing else but clicked Search templates
Resulted in my custom style being selected in the drop down
I'll keep trying for better reproduction steps though this could likely be a local problem, either my PC or that dev site.