Example:

This is what the pdf looks like in illustrator.

This is what the exact same pdf looks like when saved and opened in acrobat. (all pages look like this)

This is what the pdf looks like when linked to Indesign

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When I originally made the template in indesign, I imported the pdf, showed import options, and linked the pages to the same page number in the pdf. 1 to 1, 2 to 2, etc.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.

So I've been trying it with using an .ai instead of a pdf, and the .ai just did the same thing.... Now I'm really stumped, and also beginning to be confident that the only linking one page symptom is more an issue with illustrator.

However.... I don't think it is only illustrator. Another symptom started yesterday: Hidden layers in the linked file are being un-hidden once they are linked.

There is a gradient on every page that is used for showing white elements in the mockup, but only when they are against the background. It is hidden and in it's own group and layer in illustrator. (From left to right) This is what the pdf looks like when viewed in acrobat, then when linked in indesign, and then what it should look like when linked. (I deleted the hidden layers and resaved). Any ideas?

No, the other artists in my company use corel as a standard so I have to use bitstream for font management.

So you're saying that the visibility is not related to the other issues that I'm facing?

Yeah, I understand my problem probably can't be duplicated and is unique to the process that I go through to make the files that I use... It's hard to explain the reasoning behind all of the steps that I take but they are necessary for the final product.

I'll see what I can do about using a new user account, but I'm on a network account and I'm not sure if I'll be able to. I guess only the IT guys will know.