I am making a mod that adds some small settlements to black marsh but have run into a glitch.
I used tes4gecko to make an esm version of the heightmap, I keep a esp version that I load with oblivion and load the esm version in the CS.
When I tested the mod there was a large square of land missing in the area I modded.

Anyone know how to fix it?

You're going about this all wrong. You can't convert the heightmap ESP into an ESM, as using that in-game results in issues like large squares of land going missing. You need to ESMify the ESP instead. Now there are about three ways to do this. The quickest is to use Wrye Bash - simply right-click the ESP and select the ESMify Self option. And after editing your mod in the CS, open Wrye Bash again, right-click the ESMified ESP and select ESPify Self before launching the game.
But if you haven't got Wrye Bash installed, then take the ESM you created using Gecko, and change the ESM to say ESP - giving you an ESMified ESP. You'll need to swap this file with the original ESP whenever you want to launch the game.

Always use an ESMified ESP (not an actual ESM) when editing in the CS.
Always remember to ESPify that ESMified ESP again when using it in-game to avoid guaranteed glitches.

I have tried wrye bash but it wont open on windows 7

I'll try the second option.

Wrye Bash works fine for me in Win 7. Try installing Python and Wrye Bash again, maybe something didn't go quite right.