As far as I can see all settings are identical. Same scene. Same field of view. Same everything.
I could narrow down the difference to 34fps vs. 41fps for that scene after I deleted settings_coolvlviewer_1265.xml to make sure all debug settings got changed back to their defaults.
The scene that I use for testing has quite a lot of transparencies (windows and lots of plants). Could that be a contributing factor for how big the framerate-difference is? Maybe some difference in texture detail?
Another weird thing that I noticed while experimenting: SL's viewer gets noticeably faster when I change lighting from "Sun/Moon" to "Sun/Moon + Projectors". How can that be? It calculates more shadows and gets faster??? And no, this is not the cause for the framerate-difference that I see. RenderShadowDetail is set to 2 both in 1.26.5.9 and 3.4.1.
Don't get me wrong, 34fps are still very good. It's just my curiosity that can't let go.

The framerate is still high enough that it's a minor issue.