Is it possible that there is nothing really wrong with SEP 2 even if you use some control points on your image? My wild guess is that the adjustments available in GIMP might probably be amplifying the effect of that control points you used while inside SEP 2 and so making those concentric circle anomaly slightly visible. Normally, what I do is to use SEP then apply a mask in photoshop rather than use the control point of SEP. Not a good process but works for my taste. Apologies if I have offended you by asking about GIMP.
This is a screen capture of a control points' mask layer showing the concentric circles. This is not the actual image, this is only the masked layer showing the extent as to how far the control points' adjustment will affect the image.
http://farm7.static.flickr.com/6190/...a7fcd189_b.jpg