Thanks for the update!
A check of our database shows that we are using WQXR's record for a 610 Watt transmitter on channel 105.9. As far as I can tell, it should be showing up in the online tools correctly.
I think what is happening is that you have too many FM stations in your report. There are so many FM transmitters in some areas that a complete list might include a few hundred stations. Our reports cut off that list at around 65 rows.
My guess is that WQXR is actually being included in your analysis. If you look at the rectangular graph along the bottom of the report (frequency vs. signal strength), you will probably find WQXR-FM shown toward the right side of that graph around where 105.9 ought to be. The station is probably just too far down the list to be included in the table.
Sorry about this limitation. I'll look into ways that we might be able to provide a much longer list of stations in the future.