Hit your F11 key to see the framerate while you are playing and see if it changes a lot. The FPS will display in the upper right corner, if you see i go from llike 20 to 60 then there is an issue.
It doesn't sound right. The birds fly at basically the same speed from the start of the level to the end of the level. Obviousy as they are flying around they'll switch directions which means the will slow to a stop and reverse direction or drop down/up the screen - but the other birds would continue at the same speed while this is going on. The only other thing is the... darn I should know the name of the thing, I play this game a lot - the terradactal looking thing that comes out if you take too much time on the board, that will fly somewhat slow and then once you clear the board, it will speed up to get off the board so that the next level can start - but that doesn't sound like it is what you are talking about.