Perhaps this is what is being suggested by the error:
1. Line 2 of git-annex-autostart.vbs is failing
2. Line 2 seems to be requesting that the command "git annex assistant --autostart" be executed
3. If the failure is due to a file being failed to be located, may be the process executing the vbs file is not able to locate the executable for "git".
Since the windows support seems to be in beta, may be it's better to wait until it's more polished.