FanHouse has some information regarding the timeline of the Astros' awareness of the cyst in Brandon Lyon's right shoulder.
The Astros signed Lyon to a three-year $15 million deal to replace Jose Valverde at the back of their bullpen in December, and the team noticed the cyst in his shoulder when performing a physical on him then. According to general manager Ed Wade, the team brought Lyon in for another MRI on the shoulder, and after seeing the results they decided to move forward with the surgery.
"Brandon was experiencing some weakness and discomfort in his shoulder, and we brought him in a couple of weeks ago to be seen. At the time of his pre-signing physical, his right shoulder MRI showed a very small cyst, and when the MRI was repeated recently, it showed that the cyst had enlarged and was pressing on some nerves. Since having it drained, Brandon reports no problems, but he will be making up for a little bit of lost time when he gets to Kissimmee."
Interesting. They knew about the cyst, signed him to a big-ish deal, and went about their business. Cyst got bigger = surgery. Let's see how 2011-2012 play out.