I have used subversion for a few years, but I have not encountered this problem.
I Googled for svn: Malformed representation skeleton
and got some 200 hits.
One was on haxx as you mentioned and was eventually resolved with manual fixes.
An excerpt from another:
which suggests a serious problem. By starting over
, the poster is referring to a previous article in the series. The error message relates to that action, so it suggests to me that there is an MD5 problem in the repository.
You may want to look through some of the other 200 hits.
Let us know how it goes for you - best wishes ... cheers, makyo
( edit 1: addition )