A couple of things to note:
According to the
Gardening FAQ -
When you cross-pollinate two different plants, there is a small chance (~1%) that a mutation will occur, and the 8 seeds produced will be either bright white or black.
So your 45 plants is way to small a sample to even wonder why you haven't gotten a mutant black or white.
Also according to the FAQ -
If you are using the 2D client, you can tell immediately whether or not you've gotten a mutation, by looking at the color of the "0/8" seed counter on your plant's Reproduction gump. There is a bug in the KR Reproduction gump as of August 2008 - the seed counter is always "plain" colored - so the only way to tell if you got a mutation is to pull a seed off the plant and look at its color.
As to differences growing in a Raised Bed vs in a pot, the Raised Beds do nothing more than negate the need to "tend" the plants. They have no effect on what is grown or produced.
Just sayin....