I tried a bit of experimentation today - I used the Fallout: New Vegas version of the Geck to mess around with Fallout 3. Everything worked fine, there were no errors (unlike the Fallout 3 geck), and fun was had. However, any change I make (such as changing damage values or placing items on maps) do not show up in game.

My question is this - is there a backwards compatibility issue with the latest Geck version? I am not new to this - I can make and install basic mods quite easily. I went back and used the Fallout 3 Geck to make the same changes, and it worked fine. Is this a known issue?

This is just a guess, but the NV GECK almost certainly saves .ESP files with a newer file version than Fallout 3 recognizes. Or, to be more specific, .ESP files list their file format version in their header, and I'd expect Fallout 3 to ignore .ESP's with a file version it doesn't explicitly recognize.

Queue

Queue is right. If you look a NV esp in FONVedit it's version 1.34 and FO3 esp are version 0.94
It is not an issue, FONV geck is not an upgrade of the FO3 geck, it is a different game.