Does this file is supposed to run under Maya?
Also a readme.txt file is welcome to understand where we have to drop your directories etc…
All noobs don’t really know they have close Maya, to drop the “LightmappingTools” directory in their MayaXXX/Script directory, to launch Maya and then using the following command in the mel script editor:
source "LightmappingTools/melEngine.mel";
BatchBake ();
To tell the truth I am not fan of global variable…
Because if I install 10 melscripts with 3 global variable as your script, Maya wouldn’t be happy after each reboots 
My advise could be to create an empty node and to attach all attributes you want on it and then you can query them when you want it and they will stay in the current scene as preferences, etc…
…and l-34 :
image -w 170 -h 60 -image "F:/Lightmapping Tool - Working/Assets/LightmappingTools/logo2.png";
There is call to a picture from your path directory and not the Script directory.
It creates a double error! :shock:
For a test I created a new scene with a cube and simple plane. I combine the 2 objects, clean the history, optimize scene size.
I change the name of my object to “A”.
Also save my current scene under “test.ma”.
I select the object and click on the “Bake all now”!
And I get this message :
At 0 we try to bake A
// Warning: file: XXXXXXXXXXXXXXXX/2009-x64/scripts/LightmappingTools/melEngine.mel line 172: Starting position (15) is invalid. It must be in the range from 1 to the length of the string. Clamping index to range. //
This is only a warning , not an error, but after that there is nothing else then I do not know what it supposed happen next! :?
Scripts look interesting, then I wait for more debug on the tools

EDIT :
After deleting the Logo line I got this error too :
// Error: file: XXXXXXXXXXXXXXXX/2009-x64/scripts/LightmappingTools/melEngine.mel line 85: Cannot find procedure "miCreateDefaultNodes". //
I’m running under Window 7-64 and Maya 2009-64.