Eagle BIFs and URGENT AF-S question to birders/tele shooters/trouble shooters!

No idea if this could be a factor, but many modern glazing units include coatings that selectively block or reflect certain wavelengths. Depending on the type of glass, either the UV or IR components of daylight could be significantly reduced coming through the glass. Maybe this change in mix of light frequencies is affecting focusing.

Have you tried putting a filter on the lens? Maybe that would help.