I haven't played for a while and at the beginning I select 7 skill classes but only have access to three in game is this correct?
Nope. You have access to all your 7 chosen skills at level 0 ingame. As you level up you can further improve your skills as you see fit. Not all skills have an active component though so many of your chosen skills will be passive and thus not show up in your skill bar.
They changed that skill in 1.0.10. Mushrooms are spawned through passive procs now, no user input needed.
That is because its first level only has passively triggering effects. There was a skill that spawned spores in the past, but spawning them all the time was annoying, so as soon as the GLG team had a chance to change it so that it wouldn't require you to do so, they did it. And really, not that many skill trees have activated abilities on their starting tier; only half of them or so, which would give an average of 3~4 active skills on the start.