Adding a script to an App-V package is all fine and good (even though it doesn't support anything beyond batch file era scripting languages) but if your script consists of multiple lines and you are adding it after the fact (especially for testing purposes) you may very well find it likes to butcher the script, condensing it all down to one long line.
The solution is very simple.
Put that at the end of each line. It is the equivalent of a carriage return (enter...ish), and a new-line.
Is this a bit duct-tapey? Why yes, yes it is. But I suppose pointlessly "enhancing" the UI is a lot more important than making a sophisticated product, so get used to duct taping App-V together.