Would you mind sharing your project or at least one with the specific problem? that way i can replicate the result and see if i can help.
Here's a quick thing with a tileset made to be 16x16, at 16x16, 32x32, and 64x64 for scale.
I'm using 1.1.0, the portable version as packaged here, but the problem also exists in 0.19, 1.0.0, and 2.0.0.