In v4.1.19 we included the ability to control if a pin will connect with a thermal relief. This feature works fine as long as the pin connecting to a filled polygon is completely enclosed with that polygon. The issue that we have seen on a few orders is that on the screen the connection looks great, but when the gerbers are generated the the connection is missing. If the pins is fully enclosed in the polygon it connects to this should not happen. To help avoid this issue you should always use the Print Artwork feature found under the File menu to preview your layout before submitting your order. The Print Artwork tool will show the issue if it is present.
Please contact customer support if you have any questions.