Rather then requiring a physical press of the reset button before an upload, the Arduino Mega2560 is designed in a way that allows it to be reset by software running on a connected computer. One of the hardware flow control lines (DTR) of the ATmega8U2 is connected to the reset line of the ATmega2560 via a 100 nanofarad capacitor. When this line is asserted (taken low), the reset line drops long enough to reset the chip. The Arduino software uses this capability to allow you to upload code by simply pressing the upload button in the Arduino environment. This means that the bootloader can have a shorter timeout, as the lowering of DTR can be well-coordinated with the start of the upload.
This setup has other implications. When the Mega2560 is connected to either a computer running Mac OS X or Linux, it resets each time a connection is made to it from software (via USB). For the following half-second or so, the bootloader is running on the Mega2560. While it is programmed to ignore malformed data (i.e. anything besides an upload of new code), it will intercept the first few bytes of data sent to the board after a connection is opened. If a sketch running on the board receives one-time configuration or other data when it first starts, make sure that the software with which it communicates waits a second after opening the connection and before sending this data.
The Mega2560 contains a trace that can be cut to disable the auto-reset. The pads on either side of the trace can be soldered together to re-enable it. It's labeled "RESET-EN". You may also be able to disable the auto-reset by connecting a 110 ohm resistor from 5V to the reset line; see this forum thread for details.