I'm not sure what system you have but I've read some systems that when a remote is used to operate a light, or slide, etc. that remote has to be used to return it to it's previous state before the manual switches will work. I think it's a safety lock out feature to prevent the manual switch from being used while the remote is in use.
I've also read about the relays on the remote control board sticking. I'm someone with more knowledge will chime in but until then perhaps searching the forum will help.
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Marshall
2012 Laredo 303 TG
2010 F250 LT Super Cab, long bed, 4X4, 6.4 Turbo Diesel
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