When I upload vectors via stock submitter they quite often end up on the site under "Images (Royalty Free)", i.e. as raster images with the eps file ignored or not correctly paired with the jpeg.

I disable rater uploads under the agency settings when I am going to upload vectors but it makes no difference.

Is there anything I can do about this or is it a problem with 123RF or StockSubmitter?

It is happening due to the 123rf files processing system working incorrectly sometimes.
If you're using FTP upload mode, try switching to HTTP and vice versa.

Thanks I will give it a try. I figured it was a problem on 123's side.