The runroot plugin is overly picky about config section names.
Currently, it does this when reading its config:

count = 0
while True:
    section_name = 'path%d' % count
    if not cp.has_section(section_name):
        break
    ...
    count += 1

So, if you had sections named [path1], [path2], and [path3], none of them would be considered because of the lack of a [path0]. Likewise, if you skipped a number in the middle (perhaps because you removed an entry), then the later entries would be ignored, without so much as a warning.

Certainly admins need to be careful when creating this file, but I think this is overly picky.