I don't understand why having 1 IE window open changed the results at all, but I believe this is due to URL encoding. %22 is HTML for "
Try this:
take "www.google.com" and copy it into clipboard, and paste it into a new IE tab. What IE tries to browse to is "http://%22www.google.com%22/"
This site is also pretty cool, it shows you what text you typed and how it gets encoded into HTML URL
https://www.w3schools.com/tags/ref_urlencode.asp
So I don't think its App-V not handling it correctly (did the sequencer pick up those values on its own?). You also have to keep in mind XML formatting, I have a few packages with '&' in the shortcut (don't ask), and if I put the & directly
into the XML it doesn't work, you have to use &.
Like I said above the only thing I can't wrap my brain around is why it ever worked, but probably some nuanced thing with how iexplorer.exe was being called.