I have been running into this issue recently as well. In my case, the link is bringing up a PDF document. Perhaps the fact that it is not an HTML document, some of the object data is being discarded so that repeated calls to window.open, using the same window name, are failing.
The big downside is the FIRST time you click the link, a temporary window pops up and quickly closes before your actual link content appears. That is the main reason I included width and height above, so the window mostly appears similar to the final popup. Also WINDOW_NAME must match whatever window name you're passing to PopupSettings. The following link talks about this issue, and also links to another page where I got this crude workaround: