remove-tree causes folder corruption

We are in the process of migrating from Visual Source Safe to Bazaar at my company. We want to have a repository on a server for backup purposes, and I've been experimenting with setting things up. Today I created a repository with a couple of branches. One branch contains source code which had been copied to a folder on the server. I added the files to the branch, did a commit, and did a remove-tree to delete the files and folders since we won't actually be working on the server. The second branch contained support stuff, including documents and snapshots of development tools. I had a .bzrignore file set up to ignore object and library files in the source code branch, and accidentally copied it to the support branch as well. After adding the files and committing, I ran the remove-tree which complained about all the ignored files. The problem is that when I went to manually delete these files and folders, several folders apparently got their owner/permission info corrupted. We now cannot access these folders, delete them, or change permissions on them. Has anyone else seen this problem, and if so, how do we fix it and prevent re-occurrence? Thanks.