See Protection Diodes, page 10
Barrel jack may be unpowered and a turned off wallwart could have the effect of being a short to Gnd. Being unconnected would be different - no path to Gnd.
Hmm, one would think the reverse polarity diode would prevent that tho.
I have the thread bookmarked at home where bricking of 2560 boards was happening when folks were powering the board from 5V. The regulator used on Duemilanove boards and Promini boards was not subject to this problem.