What you are likely experiencing is delayed onset muscles soreness (DOMS). If the muscles are sore when you push on them with your fingers, or when you stretch them out, then all the more likely this is DOMS.
DOMS is caused by the damage to the muscle during eccentric contraction. (Don't worry, the body recovers from this damage.)
It is worse after the first few workouts after having not worked out in a while. Even a 2 week break can lead to DOMS after the first workout when you return. The pain from DOMS can last for approximately one week. Your muscles will adapt so that DOMS is much less of an issue after subsequent workouts.
The Wikipedia article mentions that exercise while experiencing DOMS can help alleviate the pain, and I can support this. When my muscles are sore from lifting, the soreness goes away when I play ultimate.
As long as your range of motion and flexibility isn't compromised, and it's really DOMS that you're experiencing and not a muscle strain, it should be fine to do your workout activity as scheduled.