Ok this is definitely still happening but I can't reproduce it reliably, it seems to happen totally at random.
Basically I open up an existing schema, then go to an existing command and expand it. I then click on the existing statement and delete the contents, then click on the command itself again in the left tree, then back on the statement to confirm it's still empty. I then paste in some new SQL and then once again click on the command and back to the statement and, when the problem happens, the statement is still empty. A second attempt to paste and clicking on the command and back to the statement and it sticks.
As I said it's very intermittent and I can't reproduce it reliably yet.