I wonder if there's a non-printing character in the innerText... If there is, then the Trim would still not work as it would not be empty space.
Did you say you tried aqString.Contains? If not, I would suggest looking for your baseline within the innertext. Something like
aqString.Contains(Aliases.iexplore1_new.Page.SampleDetails.Panel(2).Panel(0).Panel(0).Panel(0).Panel(21).Panel(0).Panel(80).innerText, baseline.value, 0, false)
To examine that innerText to see if there's non-printing characters, try copy/paste the contents of the property as viewed in ObjectSpy (right-click, select copy) into something like MS Word and see if that shows up anything interesting.