SPM uses neurological convention: the Left is on the Left. Lots of data are collected in radiological convention (the Left is on the Right). SPM isn't going to tell you if it is flipping or not, however the X-coordinate will be negative if SPM thinks it is in radiological and is is therefore flipping it for your viewing convenience. You should mark with vitamin E the Right side of all subjects. If you haven't done this, in order to confirm that what you are analyzing as R side in SPM actually is R side in real life, consider natural asymmetries in the brain: The right hemisphere protrudes anteriorly beyond the left, and the left hemisphere extends posteriorly beyond the right (Toga & Thompson, 2003).
Don't stress too hard about setting the origin in those funky looking EPI images. Do your best. The algorithm will take care of the rest (quite robustly, in my opinion).
Note: Do not be alarmed when you see mean functional plots widely off the anatomical SPM template during preprocessing BEFORE coregistration. The plotting during that time is arbitrary. Do be alarmed if your coregistration plots are wildly off kilter.
Note: canlab_preproc can produce a movie that displays spikes (example still below), but it is currently disabled due to time & space constraints.