I'm just moving over to New Vegas from Fallout 3 modding, and I am running into an issue regarding the G.E.C.K

When I open the G.E.C.K., load the master file, and then click the save button, I get the popup:

"You must close all open Dialog Boxes before saving."

After finding no open dialog box (moved everything around, no dialog boxes/windows are open), I decided to look it up. I saw a few people mention having this issue with Fallout 3, with no real clear fixes mentioned. I've already tried deleting both geck ini files in my documents, redownloading the G.E.C.K., and opening and closing various windows within the G.E.C.K. to see if I could find the trouble window. So far I've had no luck. I can't even edit other people's mods, so it isn't just an issue with making a new ESP file

Any ideas?

I'm new to the GECK so I'm not sure if this is new to FNV's GECK, but the preview window annoyingly counts as a pop-up. (Probably not your problem if you closed and opened the program I guess.)

I've tried that as well, still no luck though

According to the Geck wiki for Fallout 3, that issue is due to a program adding extra buttons to the dialog windows, it specifically mentions Ultramon.

if your cell view window, or object view window have any buttons on them you will get this error and need to shut off the program that is adding the buttons.

Have I told you I loved you today?
That did the trick

Further information concerning Ultramon.

While the GECK is open, right click the Ultramon icon and go to properties > compatibility.
see the list of running applications - choose GECK - check box for using full path (in case you have GECK for FO3 also on system.)
On the options page, select the diable buttons box, and dont select any others.

Now Ultramon ignores the GECK and you dont have to disable it every time.