fromtexas,
It is very doubtful that a doppler flow exam would miss a clot. It takes a clot several weeks to resolve. So, even if your discomfort had decreased a little, it should have picked up a clot, if there was one.
The usual symptoms for a clot are unilateral swelling in the limb and possibly pain in the region of the clot. If the clot is superficial, it may also present with redness, warmth, tenderness, and a palpable mass (thrombophlebitits).
It is most likely that you have some sort of musculoskeletal problem. If you have been working out, or have significantly increased your physical activity, it is most likely you have either sustained on unnoticed injury to your muscles or have an overuse type of syndrome. It is not uncommon for patients to have sore spots when dramatically increasing their physical activity.
However, if you have reasons to have a DVT (sedentary life style, restricted sitting for long period of time, as in a long plane flight/car trip, recent major surgery or hospital stay, etc) or you are concerned that you may still have a DVT, contact your physician for another evaluation.
Good luck.