I took a peek at the Essentials GroupManager example file from it's website, and noticed some slight differences that might be the cause of it. I've selected a bit of it below, to show you, the pasted yours right below it
Builder:
default: false
permissions: []
inheritance:
- default
- g:essentials_builder
- g:towny_moderator
info:
prefix: '&2'
build: true
suffix: ''
Builder:
default: true
permissions:
inheritance:
- default
info:
prefix: '&2'
build: true
suffix: ''
After a blank Permissions line, it has [] <--those. Yours don't. Also, in the builder group you've entered an extra line after the blank permissions line. This may be throwing it off, and not letting it inherit the group you specified. I also noticed in the example file, some of the inheritance lines had "g:name" instead of just "name" but some had just "name"
Also, it wouldn't hurt to try setting the Default group to Default: True and the Builder group to Default: False
That way they are in the group with the actual permissions, not in a group that inherits them.
If you do set Default to be the default group, be sure to also set them to Build: True if you wish for them to be able to build.