While I personally haven't seen any evidence that Baker's cysts are a symptoms of Lyme, it would make sense that they can be a common thing. A Baker cyst is swelling caused by fluid from the knee joint protruding to the back of the knee. So I would guess that it disappearing quickly could be explained easily too.
I would watch for any complications though - this site:
www.medicinenet.com/baker_cyst/article.htm says that the cyst can rupture and "become complicated by protrusion of fluid down the leg between the muscles of the calf (dissection)."
Unless it becomes medically necessary, you will want to avoid the use of any steroids for this though, as the use of steroids will help the Lyme spread through out the body further because it suppresses the immune system.