Basically, what Dan is telling you is the same advice I would provide in the Wanhao group.
#1 Don't use MakerBot OEM firmware on your Duplicator. That's about 6 ways of wrong even though I know that Wanhao has that listed in the update instructions.
#2 if you want to update your firmware, Use Sailfish firmware specifically edited for the Duplicator series.
#3 No surprise to see both an SD card error and combination firmware issue on an older D3 using Makerbot firmware.
As Dan pointed out, there are tons of ways this can wrong all related to a BAD SD card read. Running MakerBot firmware has dozens of reported bugs in it, and as Dan pointed out, there is a KNOWN issue that each time you print a file from SD, certain MakerBot firmware can and DOES corrupt the file. That means it prints once fine, then craps out a second time you print because the file was corrupted.
Part 2 of the problem Dan pointed out is D3 and early D4 models route the X axis motor and endstop cables directly next to the SD card reader and ribbon cable going to the mainboard. This has been corrected on the D4S and is no longer an issue per specific advice I gave to Wanhao for new models. That said, it's trivial to make a simple modification to move the X axis cables to the back right corner hole and connect to the mainboard routing them far away from the SD card reader and ribbon cable.
I included that step in a larger mod to go to flex rated cables but no reason it cannot be performed with the stock wiring.
So basically I would say do both:
#1 load Sailfish firmware instead of MakerBot
#2 move the X wiring away from the LCD ribbon cable in the front right corner of the machine to the back right corner.
In this picture, you can see BOTH the X and Y axis wires go down the right hand back corner cable path to the mainboard.