One reason for this is that some of your variants are actually duplicates of each other.
In the following example, it looks like we should have 9 variants on Etsy. However, if you were to upload this, you will find only 3 variants were uploaded.
This is due to you having duplicate variants. What Shop Uploader finds is basically 3 sets of the following. It will then proceed to ignore the duplicates and enter the last unique set. So in this case you will upload 7-9 and ignore 1-6.
