We would need some information in order to help you find a good answer.
What version of Photoshop, Bridge and what version OS are you using?
What file format are you starting with? .tif? psd?
What exactly are you using for the batch processing? A screen shot of what you are doing will help.
Let's start with those.
I just have thousands of .JPEG images. I used action palette to record my edits onto one photo then save it. I want to transfer all those edits onto the rest of my other photos. So when I go to the batch processing to apply my actions, the JPEG option always pop up and I have to manually click it. The only way for me to get rid of it was to check the "override the acton "save as" command" and it does not save my photos.
Right now, my solution is to download an auto clicker to click on the JPEG option to save the photo by letting it click on "OK"
Use File > Scripts >Image Processor or File > Automate> Image Processor Pro if you have CC