Can someone please tell me what could be wrong when initially my top unlocked/locked and softtop worked fine, then when battery went dead overnight and I jumpstarted the car the top-button and roll-bar button stay lit(red) and they don't work. I moved nothing related to the tops and top worked before battery died.
Should something get re-set to get the buttons working as radio and windows do in this car after battery disconnects?

The last information I found is:
Soft-top-controller Module codes must be re-set (Fault-code Erased) with a 38 pin cable and a diagnostic tool (Scanner) like the "MB Star System."
And that fixes the buttons.
And only dealers and few mechanics have that diagnistic scanner.

Problem Fixed :)
So if you jumpstarted your SL500 and your Top and Rollbar buttons turned red and stopped functioning just have a mechanic connect the Mercedes Diagnostic computer to your car and Clear the Fault-codes, or Re-set the fault codes. That will turn the button lights off and they start working again.
To prevent this just try to charge the battery with car OFF then disconnect the charger and start the car.