Problem with electric windows on E240

I have just replaced the battery in my 1998 E240 after the old one went completely flat. The car starts okay and after some initial problems with it not accelerating properly it now seems to be running
okay.
I have now discovered that my electric windows are not going up smoothly. I have to repeatedly press the button to move the glass. Its the same for all windows in the car.
Is this problem related to my flat battery? What should I do?
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Resyncronize the express feature.
When you raise it to the top, hold the button down for 3 seconds.
It should explain it in your owners manual.

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