Unexpected problem with links to URLs in PDFs

Hi all
I have some PDFs that contain some URLs which when hovered over or clicked behave as expected. I need to put these PDFs through our preflight software which checks and fixes things and writes out a new file. When the new PDF is viewed it no longer has active links. I can't change the preflight software but I just want to understand what's happening. The links in the PDFs are not created manually within whatever program created them (eg, Indesign) but are just make links by Acrobat/Reader (because the "Create links out of URLs option" is on) - if I turn that option off the links in the original PDFs stop working. In my tests some links still work in the new PDF but others not, but I can't see why some would and some wouldn't. Also, the links in the new PDFs that did work often didn't work the first time you opened the PDF but would the second time they were opened (after the program was restarted). The whole thing is just weird!
The text in question is selectable text in the PDF (not vectorised or rasterised) and works consistently before the file is preflighted. But if it is still selectable text in the new PDF why wouldn't Acrobat/Reader show the links as normal. What could the preflight software have possibly done that would mess up that process?
I'm checking the files in Acrobat Pro 10.1.10 (Windows), 8.3.1 and 9.5.5 on Mac.
Any suggestions appreciated.
thanks,
Iain

True. It preflights the original PDF and writes out a new file. The text in question is still selectable (not vectorised or rasterised) text in the PDF it outputs. Are there any special criteria for text that can't be made into links by Acrobat/Reader?
I have created a couple of examples that illustrate the problem - that might help pinpoint exactly where the problem is occurring - https://www.dropbox.com/s/ltqxcht9ydgh9or/examples.zip. The "proper" hyperlink (created in ID) doesn't survive the process, which I expected. The web address at the bottom of the advert is not a proper hyperlink (it stops working if you turn off the "Create links out of URLs" option) but works in the before file but not the after.

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