Checking out from a bad repository. "Failed to collect changes"

Hello,
I am evaluating TeamCity with a mercurial repository. Something is wrong with the master repository, but I haven't quite figure it out yet.
Its problem is that a full clone of the master repository cannot happen. The error always seem to be of the form: Got X bytes, expecting Y bytes.
My work around is clone to revision 1000, then subquently pull 1000 revisions at time, and for this particular branch, pull 5 revisions at time.
My coworkers work around by doing full clones from each other.

Because of this issue, TeamCity having problem initializing my project and its VCS root.
What can I do in this scenario? How can I manually bootstrap the project VCS root?
Thank you.