I'm encountered this bug several times now. I'm currently using LR 2015.4. I have a folder with a couple thousand .CR2 images, and I want to rename them using "File Naming: Custom Name - Sequence." My start number is usually 1000 to keep them all with four digits. I've tried using different start numbers, however, but no matter what I try, a small random group of images ends up with the proper new filename, plus a -2.CR2 appended to the end. This "-2" implies there's a duplicate, but how could that be if I'm renaming everything in the folder?