Please post the code where you display the toast and the name of the sub that the code is in.
I have a feeling there is a bug that is causing the toast line of code to be run over and over again and it's giving the illusion its staying on.
You can test this by adding the below line after your toast line:
ToastMessageShow("Some message that won't go away",False) '<--- this is your current line where you display the toast
Log("Ran Toast message")
Now, when the problem happens (when the toast wont close), look at the log events on the right side of the IDE and see if you now see repeating lines of "Ran Toast Message". If so, then something is causing that toast line to be run over and over - maybe a repeating event?