Hi krass, it would be helpful if you could post the .3dm model file with the objects in it that you are showing instead of only a screenshot.

But it is normal in CAD chamfers and fillets that chamfers or fillets between surfaces at different angles to each other will be different widths.

Some explanation here:
http://moi3d.com/forum/index.php?webtag=MOI&msg=10652.57
http://moi3d.com/forum/index.php?webtag=MOI&msg=9359.2

You might need to use some method other than chamfer to get what you want if you are leaving some edges unprocessed. If you chamfer all the edges including vertical ones then you'll get juncture patches where pieces meet up instead of chamfer/fillet surfaces directly running into each other.

It's hard for me to know for sure what to suggest without being able to load the file and examine your particular case though.

- Michael