Swatches duplicating/slow copying ARGH

CS 5, Illustrator 15.1.0, OS 10.6.7 Mac (Had this problem in CS4...)
This has been discussed before, and I have tried the suggested solutions (cleaning out the "bad" code: e.g. %AI5_Begin_NonPrinting), but when I have done this, it has screwed up my documents to be uneditable or information being invisible and completely unfixable.
Problem: seemingly clean document, cleaned out swatch palette. Copy an item (spot colors involved) and paste into new document (also with cleaned up swatch palette), and all the unused/deleted swatches return. In copying/pasting the process takes far far longer than it should, my indicator that something is amiss.
So far, today, this is what is happening: copy a colored box from a swatch palette cleaned document. Paste into a palette cleaned new document, it copies over swatches that are not part of the copied item (all the default swatches). I then clean out the swatch palette again on this new document. Save. Get the "HUH" (This operation cannot complete because of an unknown error. [HUH?]) error. Then copy colored box again, paste, and none of the erroneous swatches return. However, each copy/paste/save action of a simple box with PMS 485 takes a minute each.
I just discovered today that the documents that I thought were "clean" are truly not and now I am thoroughly upset since I now have a client library full of Illustrator documents that are infected bringing hours and hours and hours of rebuilding my documents if there is no solution to this problem. Please please please advise. Thank you!
If Illustrator programmers and Adobe can't fix this known problem, well they are just f*@ked up. <--------how upset am I?
http://forums.adobe.com/message/3104392#3104392
http://forums.adobe.com/message/3413499

When I do the fix of deleting the code between the %AI5_Begin_NonPrinting & End tags sometimes the file is perfect, other times I get invisible items. I manually fix the invisible items, which usually does not take very long.
The invisible items happen for me happen where set fill and stoke none at the character level and apply that to the type level for stacked strokes.
Has been almost a year since this problem originated here, and though the situation looked catasctophic at the time(total account devastation, spreading to other accounts), no issues have returned after a month of flushing out files on the server. I have fixed this problem for a number of different people, but have never had files where the problem returned, or atleast they have not emailed me back. Sorry to hear the fix I posted did not totally eradicate this beast of a problem.
Only recomendation I have is to check again that every instance of the code between the AI5 tags is removed, and that noone copies from an infected file back into a cleansed on. Sorry to hear you have this BEAST of a problem.

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