HDR and freckling

A colleague who is similarly photographic suggested we go out of an evening to take some HDR shots. I think she knows I do quite a bit of HDR and was keen to see what it was about. I got some good results but my I'm struggling with freckling in some many shots taken later in the evening. The HDR process exacerbates the problem but I can see the marks on the source images. I've cleaned the lens and am certain it's spotless, I've even cleaned my mirror but the freckling still occurs. So it could be my sensor or failing that, I'm left with the terrible prospect that it's dirt inside the lens itself. Whatever the cause, it needs to be sorted before I go away for new year. I'll try to test the theory by taking a shot that freckles on my wide-angle lens, replacing the lens and seeing if it still occurs. If it does, it's the mirror or sensor in the camera body, if not, it's the lens. At least that'll give me a better idea of where I stand.

Unless of course it's both lenses.