Time machine was just set up and is working but although my external HD's are - from the backups to be excluded time machine doesn't seem to be finding them to back them up. Why?

When you initially set up Time Machine, one of the necessary steps was to select a backup disk. Apparently that step was not completed. The disk should be exclusively dedicated to Time Machine backups. it must be formatted correctly of Time Machine cannot access it. Try reformatting it the same as your Hd is. Then reselect it in T.M. and see what happens,