I think that it is currently only you and I that have the GTX 1060 in our systems. I see that you are gaming in Windows since you mention BeamNG.Drive.
First question, are you running at 1080 or 1440? I have a Dell UltraSharp U3415W (3440 x 1440 pixels) and I too have noticed some worse performance at lower settings i.e. using a 1080 resolution. However this does not happen in all games. Witcher 3 performs better at 1080 than at 1440 however, the FPS in Guild Wars 2 takes a serious nose dive at 1080. It doesn't always seem to be logical. In Assetto Corsa, Project Cars and F1 2016 lowering the resolution increases FPS significantly.
I allowed the GeForce Experience program to optimise the settings for my games, and then I flicked the resolution to either 3440 x 1440 pixels or 2560 x 1800 pixels. I also downloaded and ran the EVGA Precision X OC program and ran it during testing as it provides an on screen overlay with FPS etc. If you don't have an EVGA card then Steam has a built in FPS counter that you can use.
It all seems a little hit and miss and I wonder if the driver in Windows isn't quite optimised for it. Worth noting is that BeamNG.Drive is in early access at the moment, so that might also be influencing things.
In general I'm quite happy with my 1060, although I am considering taking it back to the store and going for a 1070 so that it can cope with my 1440 screen a bit better. That said all games I am playing perform better on the GTX 1060 compared to my old HD 7950, with the exception of Guild Wars 2 that seem to prefer the HD 7950.
Perhaps you can post some FPS numbers from of some other games and we can compare notes.
Yeah, I have a separate Windows 7 disk for my games. Amongst them, I have BeamNG.Drive, GTA IV, GTA V, Rigs of Rods, and Minecraft. I am running a 1080p Dell as my main display and a 2002 Apple HD Cinema display as my secondary monitor. (The Apple monitor runs at an impressive 1920x1200 pixels.)
I tried tweaking things within the NVIDIA control panel. I tried the default settings, quality settings, and more. Right now, I think most are still default. Since I have an ASUS card, I downloaded the tweaking software that's meant for it, and it seems to have some overclocking options... but I only tried the "gaming" option, and I don't know how well that really helped. Also, I don't even want to have to overclock my GPU. I just want it to work as it does.
Speaking on behalf of BeamNG, I noticed something odd about its performance. One of the default maps, East Coast USA (a heavy map with lots of trees and shadows), runs nearly perfectly, with every setting on and at its highest, and in full-screen 1080p. Meanwhile, Grid Map (not the empty one; the one with stunt ramps and such, which is otherwise a very light-weight map and is one of the only ones I'd drive on when I had my 660) is a TOTAL hog. With the same settings, I get horrible stuttering and lag. I have no idea why it's like that. Lowering settings (as I mentioned) does NOT help at all. The map lags in the same way, no matter what. I wonder if I need to re-install my game or something.
As for GTA V, I was able to put every single setting in the game at its highest, and I could run it at what seemed to me like a consistent 40-60 FPS, in 1080p and in full-screen, which is just fine. I did get a few lag spikes here and there, however.
Minecraft was the odd one here. The first time I tried it (and this is totally vanilla Minecraft, without any optimizations), I put it on highest settings and achieved as much as, like, 150 FPS. Even more insane is that, on lowest settings possible, it ran at over 400 FPS. However, coming back to the game later on (after messing around in BeamNG), I noticed that, on highest settings, it didn't want to pass about 90 FPS. In fact, it dipped as low as 36 FPS sometimes. Then, on lowest settings possible, it definitely was NOT over 400 FPS. Could be that the server I was on was experiencing some lag, but I doubt it. It runs on a nice internet connection, and I was the only one on at the time. After some time, I think I put the rendering settings on medium-high and tried again - this time, with an FPS cap back on it. Solid 70 FPS. No idea why there was fluctuation there. I'm wondering what this is all about.
GTA IV is HORRIBLY optimized, so I wasn't surprised at its lag spikes and occasional stuttering... but I really was surprised that it wasn't playing substantially better with my 1060 than it was with the 660. Just like with BeamNG, I was expecting this GPU to just crush the game. (Although, it's understandable, with IV. I had a realistic cars mod that's kinda glitchy, and the game itself was never optimized well to begin with.)
I am hoping that it's the fault of the drivers and not an issue with the card. I'm also wondering if things would be better on Windows 10; though, Windows 10 + Bootcamp are known to be problematic on Mac Pros. I'll see...
Oh, and I'll try and compare FPS and such over the weekend. I'm pretty busy with school this week, and I basically don't boot into Windows until the weekend. I was only on it today because I was concerned about my card.
I'll make sure to find an FPS meter for each and every game.