A couple of things to keep in mind when trying to diagnose reasons for purple stems include: Potassium deficiency can sometimes cause it; low daytime/nighttime temperatures or big temp differences between the days/nights can cause it; genetics is sometimes the reason but most of the plants I've heard doing it genetically were 'purple' strains in the first place; I've seen it personally in a few strains either during early seedling stages, and late in flowering - which I guess is simply a maturity issue; and the list goes on.

Try to maintain a soil pH of around 6.5-6.8, and if you're going to veg it out a bit, make sure you've got a good Nitrogen source on hand to help it grow strong after the roots are established. Clones can be finicky at first, so don't force too much growth initially... they're not going to do anything until the roots allow them to. If problems get worse, try to post pictures of the symptoms you're seeing and also fill out as much of the Troubleshooting Form as you can.

Best of luck. :thumbsup: