So my problem seems to have righted itself, my level used the open world template which has two landscape layers.
The other day after encountering this issue I deleted one of the layers thinking that it could be responsible, but I still had the issue, so I deleted the landscape segments and added in a new landscape.
After having to re-sculpt the landscape I tried painting the foliage again, but found the issue still remained. Anyway, today I loaded the project and tried painting foliage and everything is now sitting correctly. Weird, it’s like it was still using the collision for the previous landscape layer. I do have another issue now though, if I sculpt the landscape all the foliage I painted before doesn’t move, So I basically have to delete it and reapply it, after that it’s ok. The engine seems a bit buggy, like my foliage brush disappeared even though I could still paint, just couldn’t see the brush size to paint with. After restarting the engine it came back.