I changed the first lot of banners to pdfs, then put them in as linked files in indesign then made the jpegs from there which worked fine for the one file with the larger banners. It took away the stitching and everything looks great. But then I did the exact same thing with the smaller banner files and attached is what has happened to four of the files! So frustrating.
I'm not seeing a problem in your screen captures—maybe your inserted captures don't have enough res to show the problem?
When you save as PDF it's still possible to flatten and get artifacts—depends on the PDF setting. Save as .ai format, which will always keep transparency live.
Also if you have situation where you are forced to flatten in AI or ID and are getting stitching, try creating a custom Flattener preset that is all rasters—then choose it in the PDF dialog. I've never seen stitching artifacts using this preset:
