Are you sure the colors were muted originally? Since a lot of Jacobean crewel was on home furnishings, it probably faded a lot, and other types of Jacobean embroidery that have been more protected seem to be pretty bright.

To quote from "Jacobean Embroidery" by Fitzwilliam and Morris,
"As I have before mentioned, a certain brilliancy characterised the work at one period, but this cannot be regarded as the best type to imitate. The most harmonious were carried out in two schemes. One had all the leaves worked in Mandarin blues, shading from darkest indigo to softest blue-grey. These were placed in juxtaposition, with tender mignonette and silvery greens, a strong accent being occasionally introduced by a flower or filling carried out in true rose leaf shade or by veinings of bronze greens and browns.

The other scheme, and this is more rarely met with, was in bronze greens throughout, intermixed with yellow and about three shades of the dull blues. Black sometimes is to be noticed in both these colour schemes, also bright and buff yellows and chestnut browns, and the colours were mostly confined to the blue scheme first named, but there are examples extant of an entire design carried out in shades of red, as in the Tudor and early 16th century hangings one finds blues responsible for the whole colouring. These vary in tone, and in the late copies of the designs the blue has a very green tinge about it.[2]

In the reign of Queen Anne taste reverted to the older lighter designs, grotesques were eliminated, massiveness gave place to grace, and brightness of colour to a soft modified brilliancy that was very engaging. In the Georgian copies heaviness again obtained favour, and gradually the designs deteriorated, and were eventually temporarily lost in "the limbo of the past."
So I guess you could say it varied over time.:-)