I have the latest version of the plugin (3.2.1) and am experiencing the same issue this: http://support.fancyproductdesigner.com/support/discussions/topics/13000001331 person was/is experiencing.
This was previously working till I removed views from a product and linked multiple FPD products to a Woocommerce product.
For proof please see attached screen capture.
In addition to the new replace layer not adhering to the set color in the color link, it is also ignoring the previously set 'Layer Position Unlockable' setting which was 'No' - once a new logo is set, it is able to be moved layers.
You have set the color link and layer position setting in the designs options as well? The replacing design does not automatically inherit all the modifcations of the old one.
Yes, in the 'Fancy Design' options, within the 'category' setting for the category, the colorlink is set. There is no option to set 'layer position' from here.