When a user has automatically accept files turned on, and receives a file that the user already has (same file name), the 'choose a name' dialogue box pops up, and places focus on the text input field requesting you to select a new name.
If the user is typing away in a message window, and a file comes in with an existing file name, the likely result is they will overwrite the contents of the 'choose a name' text input field, and lose the file name. This probably breaks a HIG rule in that pop ups shouldnt steal focus without a user action, and then give focus to an input field with existing text, hence overwriting the existing text.
In my specific case it occurs with msn (the only protocol I use with file xfer)