Something doesn't sound right at all. Unless you had the bleeder nipple out for a long time you shouldn't have lost more then a tablespoon of fluid from the res. If it was low enough to not have any in when you checked it then id say you did have an issue with the master cyl in the first place. The best piece of equip for this is a hand held vac bleeder pump for 35 bucks at any autozone. Hook it up to the nipple,remove master cyl cover and start the squeezing. It wall draw the fluid from the res down the line and into a catch can on the vac unit. Just keep adding fluid til its all new then close the nipple. Done. If there is a problem after that then its usually the master cyl.