I encountered similar issue. The missing artifacts (jar files) exists in ~/.m2 directory and somehow eclipse is unable to find it.
For example: Missing artifact org.jdom:jdom:jar:1.1:compile
I looked through this directory ~/.m2/repository/org/jdom/jdom/1.1 and I noticed there is this file _maven.repositories. I opened it using text editor and saw the following entry:
#NOTE: This is an internal implementation file, its format can be changed without prior notice.
#Wed Feb 13 17:12:29 SGT 2013
jdom-1.1.jar>central=
jdom-1.1.pom>central=
I simply removed the "central" word from the file:
#NOTE: This is an internal implementation file, its format can be changed without prior notice.
#Wed Feb 13 17:12:29 SGT 2013
jdom-1.1.jar>=
jdom-1.1.pom>=
and run Maven > Update Project from eclipse and it just worked :) Note that your file may contain other keyword instead of "central".