If you are making JPEGs, what is it about Image Processor that is any different than Save For Web? JPEG compression is no different between the two, is it? Maybe you can post an example of the differences in output between the two strategies, with the settings you used in each instance.
You may simply need to increase the quality of the compression in the Image Processor to match that of the Save for Web interface. That is, the "Quality" scale in Save for Web ranges from 0 to 100 whereas the Quality scale in Save As..., or Image Processor, ranges from 0 to 12. So, a quality of "80" in Save for Web is not a Quality of "8" in Save As or Image Processor, but a quality of 80% of 12, or 9.6, or about 10.
If you match the quality settings and then compare the results from Save for Web and Image Processor, the differences are negligible - put one result on top of another in layers and use the Difference blend mode on the top layer - you will get an almost all black result. If you drop a curves layer on top of the stack and bring the White Point all the way to the left, you can see the slight differences in the JPEG compression blocks.
So, use Image Processor with quality settings that give you the best file size versus quality and save yourself time and effort.
Hope this helps.