Thank you for your post.
FileMaker Themes do have modified Scroll Bars, but users do not have the ability to modify them via the inspector. For more information on Themes in FileMaker Pro see Knowledge Base Article #10785.
If you are seeing something more than this (not sure if you are seeing two portals with different Scroll Bar Styles?) please provide details and possibly a screen shot.
Additionally, you might add a suggestion for control of the scroll bars via the Feature Request Forum.
I hope this information is of use!
The color of the scroll bar if related to the source of the file. A portal in a converted v11 file (Classic Theme) will display the scroll bar in the "Portal Row" fill of the portal. If you change the fill of the "Portal Row" it will apply it to both the row and the scroll bar. This portal can be pasted in to any themed layout and it will retain this characteristic. However, if you save this portal as a new style in the theme, you lose the scroll bar coloration and can’t get it back.
keep on mind that Classic Theme is much slower than any "real" theme.
If you consider to build up your own theme, I can recommend Theme "Visionary" as a pretty neutral basis for your own styles.