Can you send the PSD template to me to test? There is a bug in Photoshop that causes this to happen if text layers were scaled in a certain way. I thought it only happened when using the Replace test popup window though and not in batch. So if it is happening in batch then I want to have the template to test.
I think that I know a way to fix the template. However, I want to see if I can find a work around to the Photoshop bug that I could implement in SPA. So I need a template with an affected text layer to test.