I have just started getting problems with generating manufacturing gerber files. This is something I have never had a problem with previously.
What started happening was that the gerber generator was taking much longer than normal to complete and when the output files were checked in a gerber viewer the layers were corrupt. The tracks and pads being faintly outlined with the remainder of the board still showing copper.
Having looked at the problem for hours I have found the work around which may be of help to anyone experiencing the problem until it is fixed.
Output -> Manufacturing plots -> AutoGen plots -> Sellect Setting tab
then for each layer in turn toggle the Pads-Only tick box
Then run as normal and this time it will be fast and produce gerbers that look correct in the viewer
Hope this helps if you are having this problem now, and for the developers to find and fix it.