Condensation can be the cause of the rot in your windows, but I would be more concerned about the original installation and potential water leakage/damage as well.
Before you look at repairing or replacing the windows you need someone with knowledge and experience to investigate your problem to determine if the rot is only in the window system or if it has spread into your wall system.
Unfortunately, rotting walls due to bad construction practices and incorrect window installations has reached epidemic proportions in some parts of the country and I truly hope that your problem ends up being relatively minor.
And as a follow-up, from rereading your original post I am hoping that when say bottoms
you are referring the bottom of the sash or moveable part of the window. If ONLY
the bottom of the sash is soft or shows signs of rot then you are likely okay - so far as the larger picture goes. If by bottoms
you meant the bottom of the frame or sill, then by all means get the windows/walls checked before you invest in repair or replacement.
Here is a link to Building Science Corp website. Building Science is in your neighborhood and they are nationally recognized as experts in home building and remodeling - particularly in areas of water infiltration.
It might be worth a few minutes of your time to read some of their information about water penetration behind siding and from faulty window installs.
Building Science Corporation