Used Photoshop Image processor to batch convert from CR2 to Jpeg and the edits don't stick

Ok, so I had a huge wedding where the bride paid me to deliver a ton of images.  Well, i did all my edits in ACR and then photoshop.  While in photoshop all the edits look to have been applied.  So, I use edit > Scripts>Image processor to convert the CR2 files to Jpeg in one fell Swoop.   Well, on my last run though (checking any images for missed edits or what not), none of of the edits were applied to the saved jpegs.  So I bring one up in Photoshop (the saved Jpeg) and the edits are applied in Photoshop.  So I click save and it tries to save as a PSD file (which it was not originally saved as).  I click to JPEG and it asks to replace the existing file and I do.  Voila, all the edits are a-pplied.  Now, I have about 200 images that I need to do this on. 
Is this common with the image processor?  Is it not for converting processed Raw files to JPEG and keep the edits?
I'm very frustrated since now, depending on my misunderstand of the tool, I have to spend extra time saving the files again.  (At least I don't have to re-edit them)

I have action I wrote so that on large groups of pictures I hit my actions.  It goes through the whole set.  Then I hit my flatten and it goes through the whole set.  Then I go to scripts > image processor  and covert them to jpeg. 
The weird thing is when I bring up the jpegs in photoshop, all the edits are there.  When I look through Photo Mechanic or upload them to the web, they aren't

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