File placement in folder being stubborn

So yesterday I got Toast 10 Titanium in hopes of transferring my VLC contents onto a DVD to watch through my TV. However I noticed that when I installed the programs and checked out the files, the icons were super huge! So I fixed them to have the icons identical to my other icons, however when I run OnyX diagnostics and it cleans my comp, it reverts the spacing between them to look as if they were still there when they were large. I am rather OCD when it comes to my computer, and was wondering if there is any way to stop the icons from being so stubborn, and just get placed out like all my other files in their folders? I've never seen anything like this before so it is kind of annoying. Any tips or ideas would be appreciated. Thank you.

Did you look in Show View Options(SVO) to see if the grid spacing was actually increased? Wonder what would happen if you adjusted a window the way you wanted, then click Use as Default in the SVO dialog?