awstats.pl is failing to parse perl 5.14 regexes. As a result, it is causing SkipFiles to not behave correctly. I suspect but have not verified other config file settings which support regexes will also have this issue.
I get the same behaviour with AWStats 7.1 (build 1.983) and Perl 5.14.2
This seems to be the same bug as #868 http://sourceforge.net/p/awstats/bugs/868/
At least the discussion revolves (and includes a patch fix) for the caret problem.