Why do some Harpsichords have the colors of the keys inverted?

The white keys used to be made of ivory. Over time, it became more and more expensive because ivory was very fashionable (ornaments, etc) and was difficult to obtain. There are fewer black keys than white, so reversing them and using ivory, instead of wood for the black keys, was cheaper and made the instruments less expensive to produce and buy.

Harpsichord Keys

Harpsichord (and organ) keys were often made of different types of wood and bone. There is no particular reason that keys should be any particular color over any other color. EXCEPT when pianos became popular, Ivory was used as the material for white keys because it has excellent tactile feel and wicks sweat. Ebony is often cited as the wood used for black keys, but in reality black keys are most often some other hardwood painted black.

... at this point it's just convention. (and some people find it difficult to adjust to a different visual representation)

Every once in a while a manufacturer puts out a "special edition" keyboard with reverse keys. They tend to sell out fast at a premium price, though there is nothing special about them other than the keys. http://www.hispasonic.com/noticias/korg-sv-1-black...

The best way I can tell you to differentiate between the keyboard function and the harpsichord function goes as thus: When you are playing on the harpsichord setting, it is IMPERATIVE that you have a bust of Mozart, as a child, on a horse, chewing gum. This will correct the key problem of never knowing what note will come out that Glinzek pointed out. When you are playing your keyboard on any other setting, replace Mozart with a Furbie. This should solve all of the note discrepancies! And yes, you read the music the same way.

Willem's answer is excellent. To add to it, many harpsichords had no ivory used at all. It was just too precious a material at one time. If you look carefully at some instruments you'll see the the 'white' key in the reverse color scheme are made of light colored woods like maple, ash, and even holly (very white indeed). Check out the bass pedals of the organ and you'll see the light colored woods being used (could you imagine the cost of that much ivory?!)

Several makers became quite well known for their use of these woods and used them as a sort of trademark for their work.