I have had luck by saving the map without building the nodes, and then compiling the .wad file independently of Doom Builder, using BSP 5.1.
The program can be found here: http://doombsp.sourceforge.net/
If your operating system doesn't have MS-Dos mode to run BSP with, download Dos Box from here: http://dosbox.sourceforge.net/news.php?show_news=1
Just read the information provided in the help files and on the website, and you should be able to figure out how to use it. It's pretty simple and runs dos programs real well.
Put the uncompiled map you're having trouble with into the same folder as the bsp executable files. (Note: Do not let the name of the folder contain a space, nor any of its parent directories. For example, c:\documents and settings\bsp, since it contains a space, won't work in Dos Box because it'll look for just the directory c:\documents and complain at you.... just something stupid Dos Box does, I think).
Once you mount the drive BSP is in, just type <bsp savedmap.wad newmapname.wad> (of course, replacing "savedmap" with the name of your file and "newmapname" with what you want to name the error-free, compiled file as), or if you are using regular Dos, just change the directory with the 'cd' command followed by <bsp savedmap.wad newmapname.wad>.
If it says "saved wad as whatever.wad" then it probably worked. Hope this helps someone! :)