Check what you have set for 'Settings | Site Options | Links tab | Section Group | Include Parent Meta Content in Each Section'.

Selecting 'True' here means that the meta keywords for a section will be included into the list of keywords for all sub-sections within that section and will sort all keywords alphabetically.

Selecting 'False' means that the keywords set on that section only will be displayed and will not be sorted.
The above is for v8 and later. For v7 go to 'Design | Options | Sections | Include Meta Keywords from All Parent Sections'.