Yes, they look the same. Strip out the :xx (length) at the start. Strip out the checksum at the end. Wrap the 16-byte lines. You then get:
E00000 0D94F6F20D941FF30D941FF30D941FF30D941FF30D941FF30D941FF30D941FF3
E00000 0D94F6F20D941FF30D941FF30D941FF30D941FF30D941FF30D941FF30D941FF3
I don't know if there is an easy way but some text munging program that does that automatically should let you directly compare them.
When you start up the Mega with the debug monitor open, do you see "stkv2" appear on the screen?