Maybe you're in panic, but this is all a bit confusing.
To start somewhere, the topic header
Cannot empty checkout
makes no sense. Checkout can't be "emptied" anyway. Guess it's about the cart...
bettston wrote: if you add items to the cart it seems to work ok, but if you leave them there the cart never empties
That alone is not a problem. It's certainly a good thing if things stay in the cart when you leave them there. When carts are being "auto-emptied" can be set in the backend.
bettston wrote: when you then try to manually remove products you get the message cart empty.
That's also good and normal: you remove all from the cart, and then it's empty. You're being told - cool.
bettston wrote: If however I add a new product to the cart I can them remove the old stuff
Why... you said already before that "when you try to manually remove products you get the message cart empty".
bettston wrote: Please help.
Help with what? Please understand that help can only be given if it's clearly described what for.
If your cart doesn't empty, e.g. something being removed, you getting the message cart is empty but the item is still in, then just say so. It's what I'm guessing your problem is, but please confirm, or please tell what it is.
If this is the problem, is that for only one particular user? Or for any (new) user and new add-to-cart actions?