I keep trying to change my foreground and background colors for just one specific session in CRT 3.4 (or later), but when I do, the colors for all of my sessions change. This didn't happen in 2.x versions. Am I doing something wrong?

Probably, when you attempt to change the session colors, you are actually changing the values for foreground and background color for one of the globally defined color schemes.

To have each session use a different combination of foreground and background colors, you need to create a color scheme for each color combination you want to use.

For example, if "Session1" is using a custom color scheme named "blue-black" and you want another session to have a red foreground and a black background, you would create a new color scheme (e.g., named "red-black") and have Session2 use that color scheme.