First, there's absolutely nothing a remote can do to mess up the hardware in your TV. But assuming that what you say above is accurate, the only thing I can think of is that for some reason the TV does not bother to do a proper degauss when it receives a discrete Power On. Which would be very odd software bug. Are the sounds the TV makes when turning on any different between the two codes?

But with that said, as Rob says, the need for constant degaussing is likely coming from an outside source, such as speakers, other equipment, or perhaps something else magnetized that's near the set. It also could be that the set is merely sensitive to magnetic north. I went through three Philips 34" sets until I found one that wasn't overly sensitive to facing south - all the others had bad discoloration, especially in the reds, unless facing west.