Quarterhoarse,
I think you are neglecting a very important piece of the puzzle. MegaTune has an number of "INI" files, one for each code version for each processor. The INI files defines where values are sent in MegaSquirt's memory, and how they are interpreted by MegaTune when they come from MegaSquirt.
You MUST activate the appropriate INI file for your code, otherwise you WILL corrupt the code, and the engine will not run properly.
So you need to reload the code you wish to use. Then BEFORE opening MegaTune and sending any values, or attempting to start the vehicle, you need to activate the appropriate INI file. It sounds like you were using MSnS-E code (there are several dozen versions), so you need to activate the INI file to match the aporticualr code you have installed. See the MSnS-E site for the details on how to do this:
http://megasquirt.sourceforge.net/extra/
You can also get the firmware (.S19 file) from that site.
Lance.