Jon,
If you prescribe a drug and get all the way to setting it up for one more click, if you don't send (I do it all the time time -- I don't know why) it will show up on transaction page and in note. Make sure you hit send script again.
We cut down on this problem by going to the new work flow which I think everyone should try:
Write script --> get to the very end of the script -- let AC crash (you have no choice) --> restart AC -- it says already running (you are close now) --> open again and resurrect last note, then open script writer --> write sig (have it disappear two or three times) -- fix that with copy and past (I always copy and paste long sigs) (once AC knows you have done that, it will no longer delete your sig) send script.
Please don't thank me for the workflow but it is beautiful and if done correctly only takes about 80 seconds.