First, it's helpful to always identify what version of InDesign you're using and your platform.
Since this is not a reported problem for most people, let's start with a couple troubleshooting basics:
You should restore your InDesign preferences. Here's a short tutorial: http://pfl.com/trb
Also, does this happen only in one file or in many? If you've only experienced it in your current file, there could be some file corruption. You might try exporting an IDML file: http://www.pfl.com/cidf
Ah yes, sorry
Windows 7 x64 platform
I have tried breaking up the file into smaller chunks but the problem persists.
The IDML solution did not solve the problem it does transfers the issue to the new indesign file, and the bookmarks in the IDML generated Indesign file are the same as they were in the PDF, deleting wrong bookmarks and reinserting them in the correct location fixes the issue within Indesign, but an export of the PDF file results in newly garbled bookmarks, it would be nice to be able to edit a bookmark location in indesign, but it does not look to be a possibility, so deleting and reinserting seems the only option.
I'd really prefer not having to remake the whole thing from scratch.
To solve the issue on a short term basis I exported it to a PDF and started from the top to set new destinations on the incorrect bookmarks, added in new destinations for links that did not work and directed the buttons to them...
Also once the PDF is opened with acrobat reader (9) it sees all the buttons as a form to be filled out, but securing the document preventing filling out forms solves this.
I have now also tried to delete my preference file, and export still garbles my bookmarks.
Hmm.. Is it an issue if more than one bookmark sends you to the same page? i have added extra bookmarks on some pages because some different information is present on the same spread but depending on the audience they may be looking for one or the other...