When I click on a link that opens up a new window, the window is over-magnified and I cannot view the whole page.
On some pages, when I click on a link that is supposed to open a new window, the new window will open with the content magnified and improperly justified. For example, I click on a link that is supposed to display a printable membership card and the card is very large and pushed to the right edge of the window so that only a portion is display. When I zoom out the window, the parent window content shrinks as does the content in the popup window, but the justification is still an issue and I still cannot see the full image.
I had to open the parent window in Chrome and bring up the membership card window within Chrome. It displayed fine in Chrome.
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Normally zoom level changes are applied to all pages on the same site (same host name here: http://hostname/blah/blah.html). So it's odd to get such divergent sizes on the same site if it was not designed that way.
Does the popup contain a normal web page, or image or PDF content?
With images, when Firefox displays large images stand-alone, the mouse pointer often changes to a magnifier to let you switch between fit-to-window and full-size by clicking the image.
PDFs can be displayed stand-alone (Firefox's built-in PDF viewer takes over the whole tab) or embedded in the page. Either way, Firefox's built-in PDF viewer has a black toolbar with zoom buttons to adjust the size of the PDF content within the viewer, but the viewer usually is not off-center.
Hmm... is it something you can provide a link to? It sounds as though an account is required for that particular site.
You can remove all data stored in Firefox from a specific domain via "Forget About This Site" in the right-click context menu of an history entry ("History -> Show All History" or "View -> Sidebar -> History").
Using "Forget About This Site" will remove all data stored in Firefox from that domain like bookmarks and history and cookies and passwords and cache and exceptions, so be cautious. If you have a password or other data from that domain that you do not want to lose then make sure to backup this data or make a note.
You can't recover from this 'forget' unless you have a backup of involved files.
If you revisit a 'forgotten' website then data from that website will be saved once again.