None of the windows will operate by using switches (master or individual door). All of the windows will operate together with key fob. Replaced master switch in door, but still won't work without key fob, Also, door locks stop working with fob with new master switch installed.

 

Did you use an OEM part? Also there are differences in the part for different model years, for example:

Honda part number 35750-SDA-A12, was superseded by Honda part number 35754-SDA-306 (revised part); both will work for a 2003-04 EX sedan.

Honda part number 35750-SDA-A14, was superseded by Honda part number 35754-SDA-309 (revised part); will work for 2005-07 EX sedan.

The electrical circuit diagrams shows a difference.

 

I ordered the part from hondafactoryparts.com for a 2007 Accord LX and received part #35754-SDA-405. The website said it was compatible for my year and model. It has the Honda Genuine Parts sticker on it.