If it stops the macro when you're not channelling wouldn't that mean it would never try and cast anything? (as you won't get to the casting part in order to be channelling something and let the macro continue)

Your original macro shouldn't have been interupting Flash Heal though, I'm pretty sure it should return "Another action is in progress" error instead, unless you've got an addon that automatically adds /stopcasting to your spells. A spell like flahs heal has a cast, pennance has a channel, [channelling] won't return true if you are mid flash heal cast.

The "not ready" message could be because it is picking pennance in the random part (which is still on cooldown), just because something is on cooldown doesn't mean that /random will skip it over. Every so often my mages polymorph spells will have their name changed (I have /cast random sheep, pig and turtle), this means sometimes I can be pressing the button and nothing happens as it's trying to cast an invalid spell, it won't necessarily pick the one that is available (/working) as the spell to cast.

You could try adding a few empty commas (just for fun) or a couple more flash heals (to give the macro more chance of picking that when pennance is on cooldown.

When my priest was disc spec I tended to save pennance for when I really needed to get someones health up fast, any way you could put pennance on a modifier and just use it when you need a bit of a boost in healing?

Or the mulitple /click thing (written up extensively elsewhere) might help, you have one key (which you're mashing) to /click on a pennance and flash heal macro button (hidden elsewhere), the flash heal button is just /cast [target=focus] Flash Heal, the pennance one is /castsequence [target=focus] pennance, , , , , , (lots of commas depending on how fast you spam the button).