How to avoid lines left behind after effects have been flattened in CS6?

Question

We work in a packaging environment using MAC OS 10.6.8 using Illustrator CS6.
In order to ouput Illustrator files correctly through a RIP, we expand all effects (shadow, glows, etc) before converting them to a Hi Resolution PDF to impose for output.
What we have started to see is lines starting to show up on the PDFs (and the Printing Plates too) where the bounding box of the effect used to be. We have seen lines show up in earler versions of Illustrator but not to the number or thickness they seem to be in CS6.
Is there any way to avoid these lines from showing up (and being printed)?  What methods do other people use to get around this issue?
Any suggestions would be most helpful.
Many Thanks
Andrew

Answer 1

So we have been working through the above issue....
Problem:
1) This problem started because Illustrator Effects wont print through our RIP unless they are flattened first.
2) The issue is further complicated by the fact that most of the effects involve spot colours (either directly or under the effect)
3) The RIP will only read PDFs saved in PDF 1.3 (Acrobat 4). Yes, we have checked with the supplier and it IS up to date!
4) When sending PDFs through our RIP from Illustrator CS6 we get white bounding boxes around spot color effects and keylines around CMYK objects.
5) These line and boxes are visible on the PDF and print on the plate.
Solution:
1) Work the file in the usual manner then split the file into 2 (or more) layers. The top layer for elements/objects/type that have NO effect on it that you wish to remain in vector format (or that can be editable at a later date). The bottom layer for ALL other items with effects applied and any items that will be modified by above effects (items below shadows or glows etc).
2) Save a PDF copy of the Bottom layer as PDF version 1.7 to maximise compatibility. Keep the other settings as you would normally use for Hi Res or custom output.
3) Split you PDF in the CMYK and seperate Spot colours. (We used Prinect PDF Toolbox to remove unwanted colours).
4) You will also need to convert all spot collours to a sigle process colour (ie we use Black) this can also be done through Prinect PDF Toolbox. If this is not done, the colour will split into CMYK at the next stage.
5) Open all of you now modified PDF files in Photoshop (the CMYK with the Spot colours removed and the Spots with all the CMYK removed)
6) Drag your spot files into the CMYK version (from the Layers Pallete). You will then need to duplicate the Black Channels and save them as Spot Channels (let me know if you need help to do this) then remove the original black layers.
7) Save this new file as a Photoshop PSD file.
8) Place this new PSD in the you Illustrator file in the same position as the layer that you originally saved as a PDF. You can now hide the original export layer.
9) Output the File as a PDF 1.3 (Acrobat 4) in your usual Hi Res method. (We do this through InDesign so that we can include our custom Slug information).
10) The RIP will now not have to process each of the Effects, just 1 single Photoshop PSD in the background of each file.
I know this is more of a work-around than a solution the the problem... but it's the only thing we know of that guarentees a succsessful result every time.
If anybody reading this knows of any other solutions, please let us know.
Many thanks
Andrew