Disabling the Composite Extension on Linux systems that work with xorg-x11 packages of version 7.3 also avoids "X Error" messages that are shown while starting or closing EAGLE 5.x in a bash window.

In the case the display gets corrupted when scrolling up or down in one of the Editor windows or in the EAGLE Control Panel, set the environment variable XLIB_SKIP_ARGB_VISUALS to 1.
This can be done, for example, with the help of a shell script:

  #!/bin/sh
 export XLIB_SKIP_ARGB_VISUALS=1 
 /usr/bin/eagle

Special note concerning the Schematic Editor:
The default grid of 100 mil should not be changed! If you prefer to work with millimeters there is nothing to be said against it. Change it in the SCH: section in eagle.scr:

GRID DEFAULT MM;

GRID MM 2.54;

If the message is Please define replacement for layer xxx in LAYERS.NEW, the layout/schematic/library contains self-defined additional layers. Due to the new layer definition which was introduced from EAGLE 2.05 to EAGLE 2.60 you have to substitute the old layer number with a new one which is higher than 100. Please edit the file LAYERS.NEW with a simple text editor and add the new layer number. If you want to change, for example, the layer number 55 to 105, please add a new line at the end of the file.
This can look like this:

55    105

How to correct the position simplest?
With the MOVE command and the input of coordinates, directly in the command line of the Schematic, Symbol, or Device Editor, for example: MOVE (0.0092 1.001) (0 1);
Since version 4.1 EAGLE allows to use the combination of Ctrl + MOVE. Select the MOVE command, hold the Ctrl key pressed, and click onto an object in order to bring its origin point into the currently active grid. Adjust the grid to 0.1 inch before.
If there are no elements or only a few in the Schematic's default grid, you could use an ULP: snap-on-grid-sch.ulp snaps all elements in the Schematic to a given grid. The same can be done for pins in the Symbol Editor with the help of snap-pin-in-symbol.ulp.

Please keep in mind:
Moving a net onto a pin does not result in a connection. You have to move the part (pin) onto the net to get them connected.
Copying a net with the COPY command and moving it onto a pin does not result in a connection (the same as MOVE). Attention: The net name remains unchanged with COPY!
The SHOW command highlights pin and net, if connected.
Nets are drawn with the NET command!