@Jeronimo88 The configs the new tool generates contain the same gcodes as the old version, just in a slightly different order. There is a bit more use of variables to calculate I do need to update the wiki guide for using it, which is still based on the old version.
There was an error in the config tool recently, where G1 H2 moves were used in homing macros, which is incorrect for CoreXY. You may have just been unlucky to encounter this. It's fixed now, so you could generate a new set. Upload the 'configtool.json' to the configuration tool, and your settings should be imported, though any subsequent changes you have made to config.g and other files will be lost.
Ian