Multi-page pdf not linking properly

I have a 6-page interactive indd template that I have been using for months without any issues (well, not these at least), but recently it has been not linking multi page pdfs properly. The pdf that I use is always saved from illustrator cs6 and correlates page to page with the indesign file; page 1 in the pdf links with page 1 in the indd and so on... The issue I am having is that almost every other time I link the file up it behaves differently. Sometimes it will link one page of the pdf to all of the pages of the indd while showing that they are linked to different pages, other times it will not show up at all on the pages, but will show that it is linked in the links panel. Sometimes it will only link one of the pages up and leave the other 5 blank or it will link the pages up with some sort of transparency...
Now, I am not sure if this is a problem with Illustrator or Indesign because of another symptom: Sometimes when I save the file as a pdf it saves as if it is not a multi-page pdf with different content on every page, but rather a multi-page pdf with every page being a zoomed-out view of all of the artboards together but with only some of the content showing (only artboard 3 and 4, only artboard 6 and half of 1) when it is opened in acrobat. Also, sometimes the pdf when viewed in acrobat looks perfect, but when linked it only does a few of the pages in indesign.
Long story short, this doesn't make any sense... I know this is hard to follow and I don't understand why or how it is happening because it seems that every time has a different issue.
I know that you'll probably have questions and I’ll do my best to answer them, but I'm afraid that uploading files for samples won't work because there appears to be nothing wrong with the files themselves... just the links and/or export.
Win7, CS6 , 12 gigs RAM, i5

I have been using this method successfully for quite some time with these exact files, only in the last few days has this problem shown up.
When I originally made the template in indesign, I imported the pdf, showed import options, and linked the pages to the same page number in the pdf. 1 to 1, 2 to 2, etc. My original thought was that this setting had been lost, so deleted the linked pdf and imported it again to try to get the 1 to 1 link. However, that did not change anything and I noticed that the page that shows up by itself in the pdf is almost always page 2, not page 1. If the page-to-page connection had been lost, all of the pages in indesign would be linking to page 1 as is the default behavior for linked pdfs.
Also, I thought that the save issue would be on the illustrator side too, so I tried resaving it but that didn't work either. The only way that I can get the file to work is if I remake it completely and save over the old file.
Now, I know that you're most likely thinking that this is an illustrator issue, but I don't think that it is one or the other, but rather both of them. The screenshots that I attached above are not the only way this error manifests itself. Sometimes the pdf looks right in acrobat, but once it is linked it displays with a transparency, shows only a few of the pages, or shows none at all.
I'm probably going in circles here, but I cannot figure out which program is the cause of the error or if there are two different issues that are happening at the same time.

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