Locks and Windows not working

the battery went dead on my 99 Sub, I put the charger on it but when I opened the door some relay or something under the dash started clicking and the dome lights were flickering on and off. So I just closed the door thinking this was due to the low battery sich. Then out of habbit I tried to lock teh doors with the remote...again not enough power. Fast forward to the next morning...all is well, the battery is charged she starts right up,but now the key fob wont unlock/lock the doors and the windows will only operate form the master on the drivers door...HELP!

when you battery dies the computer resets so you have to reprogram your remote, check you cars handbook if you have one. It will show you how to reprogram you fob.