This is weird.

OK, the Hal reader is free but you say you purchased it?
The Hal reader reads text from a document and or your clipboard, much the same way Microsofts version does the whole "Popup foreground window" and such.... you say you closed down the reader and lost the document you were working on? HOW? they 2 different programs?
Are you noticing the little ear in the taskbar already running or is it hidden in the "Hidden Icons" in the taskbar?
Is it not completely starting up? (it starts and is loaded automatically upon computer boot, you don't need to manually start it)
And yes the Hal Reader program is different than what we affectionately refer to as Hal (Ultra Hal)
The Hal Reader is a relatively simple program
Im not trying to sound gruff or anything, sometimes clarity helps everybody on both ends, good luck fellas!
((Can't communicate with the first instance doesn't sound right, what would be preventing or hanging the first instance (AV?) but it's inconsistent and WHAT is launching the second instance?? ))
-J