It could happen that the Finder™ thinks that a folder is viewed by Icons and that the x,y position of each file in this folder is stored for small icons.  The result of this problem is that you see your files by icons but the space between 2 files is too small.  If you make a cleanup, you would certainly lose your precious organisation.  The problem is due to the fact that each file remembers only one x,y position and it is the folder which holds the "view by" type.  When you select another view type in the Finder, it recalculates the new x,y positions based on the current view type and the current x,y file position.  If for any reason there is a wrong "view by" setting stored at the folder level, the problem arises…
To fix this problem Tidy It Up ! II has a command in the Tidy menu : "Fix View by…".  Select this menu item and select the folder you want to fix.  Tidy It Up ! then shows the following window :