Hello, i just made an entire dungeon, and suddenly, i duplicated one more piece and for some reason it dropped a little bit, and is now impossible to align properly.

How do i rectify this?

I'm using the dwemer genkit.

you can double-click on it, and double-click on a piece next to it.
Look at the Z Position and adjust the one out of whack with the one that is right.

I am building a player house and have found many peices that do not snap together even from within the same kits. Not sure if it is from placing a piece (the one you wish to snap to) with snap to grid turned off then trying to snap to that one. Also even peices that require spacers like floors and ceilings don't often snap either so to get around this I copy and paste the x,y, and z coordinates from one piece to another to help align pieces that won't snap. It is trial and error sometimes as it also depends on the orientation of a piece etc. I'll also try to use duplicted sections that are already 'snapped' to create other parts to speed up the process a bit. Another way of doing it is to zoom in to the area you are trying to match up and adjust the coordinates till the pieces line up I usually set the modifier at 0.1 or 0.05 for the ones that won't go by hand. Hope that is helpful. I know it is tedious but I haven't yet figured out exactly what dictates what will snap together other than being of the same kit (which doesn't always seem to work anyways).

Unfortunately it's exactly the same piece as the piece next to it, at exactly the same orientation. I've already built the dungeon with mroe than 100 pieces, and more than 30 of that particular piece. It's only the Z axis that doesn't want to align for some reason.

Williesea's idea works, but i don't want to have to do that each time :/

Try changing your snap to reference, which you can do by clicking into your render window, hitting shift+q, and clicking on a piece you want to align the other piece with. This technique is detailed in the tutorial found here: http://www.creationkit.com/Bethesda_Tutorial_Layout_Part_2 under the section named "Working off the grid."

If it's still not aligning properly, you may need to change the number of units you are snapping to in the file>preferences window in the movement tab in the "snap to grid/angle" fields.