I think YJ is right about the speed. Many putts can and should drop in from the high side of the hole on the ones that break significantly and they won't if the speed is too high.
I don't think the ball will affect your putting - AFAIK they all putt the same.
Also - sometimes it seems like these things come in spurts - today I missed a lot of med-long putts by fractions of an inch on the low side and the high side. Some days they drop - some days they don't.
And yes, things get harder as you tier up. I don't remember exactly when green speeds change - but they continue to rise and your tee boxes will start to creep backwards!