It turns out that the problem was not caused by VMware Tools. It is more likely that the windows Application Experience service caused this issue, but I am not positive. I ultimately resolved the issue by adding a virtual disk and creating a new share, then pointing the build to look to this share. If the build step leaves an open handle for this share, it wont affect the subsequent step which does not refer to that share again (previously everything was done from the same share, so if there was an open handle, file operations would fail).