This issue is a bit strange and I'm not totally sure it's sublemacspro or ST3 causing it but when I upgraded to the latest sublemacspro version on ST3, incremental searches are now highlighting the found text using my theme's color settings for Strings instead of the color setting for selections.
When I disable sublemacspro and do an incremental search, the color used is correct. I've tried using multiple themes and the issue doesn't seem to be specific to the theme I'm using.
I tried to track down what caused this in sublemacspro's package but all I found was that if I commented out https://github.com/grundprinzip/sublemacspro/blob/master/Default.sublime-keymap#L99 then that made the problem go away (at the price of the incremental search key mapping no longer working..).
Adding fixes for #79, #78, and #80
This should be fixed in 2.0.4 that should be available soon in ST via package control. Please let me know if this helped.
When I wrote the i-search code I was trying to figure out how to make it look like the built-in i-search. My highlighted search strings were always yellow until I completed the search, at which point they became the selection color. So I found "string" as the scope that matched the color Sublime was using itself.
I think it's important that the selection (multiple cursors and all) are differentiated from an in-progress search where you are assigning matches as you go to future cursors. Like CMD-D in vanilla ST except that i-search lets you have non-contiguous selections.
It should be possible to see what sublime is using for the scope selector, right? Let me see if I can confirm my choice.
I think it's time to close this. My colors exactly match the default colors. If you think I have made a mistake, let me know.