Are you trying to run those batch scripts on a multi-user system, perhaps even
from a limited (non-admin) account? When I attempt to run a new batch file on
my Admin authority account, MSAS initially asks me to allow it, then adds it to
the allowed scripts list, and continues to let me run it across re-boots, but
all from the installing account.
MSAS Beta1 was never designed to run in a multi-user environment, particularly
on accounts that did not install the application originally. We expect changes
to that behavior in Beta2, but if this describes the problem, you might try
authorizing the batch files on the installing admin account, and then in MSAS
Settings > Alerts > Allowed alerts, uncheck Enable allowed alerts.
That just might work for you until Beta2 arrives.