firmware starting too slowly

I've built the reprap motherboard circuit on a breadboard and uploaded the firmware to communicate with ReplicatorG, but it won't connect. ReplicatorG successfully resets the atmega644p, but it fails to initialize. ReplicatorG says:

Reset.
No connection; trying to pulse RTS to reset device.
Unable to connect to firmware.

I hooked up a second serial adapter to monitor the communication to try to find the problem, and I found that the chip sends "R3G Master v106" back after the reset, but not until a second or two after ReplicatorG says that it's unable to connect.

I have tried both with the 1.6 firmware that ReplicatorG installs and the G3Firmware from github (this one says "start" instead, but has the same problem). What could be causing this? I haven't built some of the components outside the motherboard yet, could this be delaying the startup? Is there any way to make ReplicatorG wait longer for the firmware to boot?

The original Arduino bootloader would wait up to 10 seconds after a reset for a possible "download this new program" command, before turning control over to the previously downloaded program. Newer Arduino models reduced that wait to 1 second (and provided a means for the host to force a reset). Perhaps the bootloader in your Sanguino chip is the older variety? That's just a guess.

On the motherboard of my MakerBot I found that jumpering the holes labeled "auto reset" (near the serial connector) helped in downloading new firmware.

That gave me the idea to see if it would connect without resetting (I had tried disabling autoreset previously, but only to reset manually at different times). Using the version uploaded by ReplicatorG, this works.

Does anyone know what the difference is between this and the FiveD_GCode_Interpreter version, and if there's a way to make that one work with ReplicatorG? Does the Makerbot version work with a stepper driven extruder? That's what I was planning to build, but I can't find a setting for it.