I could be wrong, but I believe that is the game changing your circle to accommodate the army number. If you make your circle larger, where no accommodation is necessary, then they stay intact. Anyone with more experience want to chime in here?
I had this problem several times. there is an easy solution. save your file as normal svg instead of inkscape svg, which is the default save file. for some reason it is more compatible with warlight editor and circles shouldn't change their shape.
also few extra nodes could perhaps help? If I am not wrong, Inkscape is using only 4 nodes to create circle. Perhaps if u add more (like 8 or even 16 in total) your circle should be less prone to being twisted?