I like the new ground and grass. The background tiles would probably look slightly better if the contrast between the two colors was reduced.
The bamboo seriously needs to be darkened. That's pretty much the only reason it clashes; it's way too bright.
I like the shading on the rocks, but the outlines need to be smoothed - you should almost never have four or more black pixels in one 3x3 area (this means all your lines should be one pixel thick at all times, and no two lines should be very close). I know rocks are generally somewhat jagged, but you can't convey that much detail in such a small space, and trying to do so anyway will just make things look messy.
The door on the rock house would look better if it were either just a normally-shaped door or just a doorway with no door. Not sure what those lines around it are supposed to be. The window also needs to be more uniform in shape. When you're carving houses out of trees or rocks or pretty much anything else, it's generally best to leave the unusual shape to the original material and make any added objects look like they would on a normal house.
If that big smooth rock thing is a part of the modular pagoda, it should be made slightly less smooth for consistency with the other rock house. On the same note, a texture of uniform straight lines makes no sense for a rock.
The background bamboo should be decreased in thickness. If it's far enough away to look shorter, it's far enough away to look thinner as well.
That said, looks great for a first/second tileset, and not too bad even independent of that.