if there is a win registry entry
HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Command Processor and its AutoRun property is to execute cd \
then the builder (ant) will be started in c:\ or d:\ instead of in the correct working copy directory path - and the builder will not find the files it is looking for.

Bamboo should make sure that the builder/build script is executed in the right directory. ATM bamboo assumes that there are not default commands run when a command shell is opened.

This directory is known to bamboo - for example
Starting to build 'TESTCI - TESTCIPLAN'
... running command line: D:\devtools\apache-ant-1.7.1\bin\ant.bat -f build.xml -debug build
... in : D:\Bamboo\bamboo-home\xml-data\build-dir\TESTCI-TESTCIKEY\build
... using java.home: D:\devtools\Java\jdk1.5.0_17

A good place to read about the registry setting for the command shell : http://www.msfn.org/board/lofiversion/index.php/t45360.html