I tested the Mega2560 w/ 1.0.3 under Windows, and same result -- about a 8-9sec delay between the reset and the sketch start (I was timing a bit more carefully), except when the serial monitor window is set to 57600, in which case ther is no noticeable delay.
I also tested it under 0023, and same result, so that means it's consistent with 0023,1.0.2 and 1.0.3.
So the interaction problem seems to have been introduced with the new version of the Mega2560 bootloader, rather than in any recent version of the IDE itself (and as noted previously, the interaction only occurs with the IDE, as the delay isn't observable running Putty, etc.)
Update:
No observable delay with Mega2560 bootloader testing with 1.0.1 or 1.5.1r2 under Win 7 (64 bit).