Hi and welcome to the forum! I am glad that I can help you.
You would like to know whether pain in the legs and behind the knee is always an indication of atherosclerosis or thrombus.
Pain in legs may appear due to muscle pain because of exercising, neuralgia, injury, vein thrombosis, acute thrombus obstruction of an artery and atherosclerosis. Vein thrombosis may appear as a consequence to pregnancies. Acute thrombus obstruction is an urgent condition and if not treated on time within several hours may lead to ischemia and gangrene.
Given the data that you described, you may be experiencing the pain in your legs due to any of the conditions listed above. Since the vascular conditions such as acute thrombus obstruction (more), atherosclerosis and vein trombosis(less) are urgent and critical, you may consider seeing a vascular surgeon to rule out or confirm these conditions. Doppler ultrasound is needed for diagnosing these three conditions. If diagnosed with any of these two conditions, you may consider having a surgery. If any of the conditions listed above is ruled out and the pain is considered as muscle pain, you may consider reducing the amount and the time of your exercises and may consider using pain killers.
Please keep in mind that I provide medical information only. I am not able to diagnose medical conditions online. Please contact your doctor or other qualified healthcare provider such as a vascular surgeon for any further advice and information about diagnosis and treatment options.