I do have a mkII for in circuit programming, although I had hoped that using arduino would mean I could leave it collecting dust And thanks for the advice about not doing 100 before I do a working prototype, I will definitely do that. It's good to know that I can at least change the time the bootloader waits for powerup. I am not entirely clear on how the bootloader can change the timing for reset, but I assume it's just outputting 5V through a resistor into a capacitor connected to reset?
Actually (sorry, I'm new to the arduino platform), there appears to be an option for using the arduino "as an ISP". Does that mean I can burn a bootloader by using the existing bootloader? Huh? If that was the case, I'd be pretty excited, because then at least it's just a two-step programming operation that I could script to happen from a single command without having to do multiple wiring jobs.
Thanks for that debug info Coding Badly. It outputs a lot of stuff, but it scrolls by quickly and the buffer isn't long enough to see the beginning by the end... do you know if I can make it send the debug output to a file? In any case, I captured it in the terminal and this is what it said:
avrdude: Version 5.10, compiled on Mar 23 2010 at 15:05:31
    Copyright (c) 2000-2005 Brian Dean, http://www.bdmicro.com/
    Copyright (c) 2007-2009 Joerg Wunsch
    System wide configuration file is "/etc/avrdude.conf"
    User configuration file is "/home/neltnerb/.avrduderc"
    User configuration file does not exist or is not a regular file, skipping
    Using Port           : /dev/ttyUSB0
    Using Programmer        : arduino
    Overriding Baud Rate      : 57600
avrdude: Send: 0 [30] Â [20]
avrdude: Send: 0 [30] Â [20]
avrdude: Send: 0 [30] Â [20]
avrdude: Recv: . [14]
avrdude: Recv: . [10]
    AVR Part            : ATMEGA328P
    Chip Erase delay        : 9000 us
    PAGEL             : PD7
    BS2              : PC2
    RESET disposition       : dedicated
    RETRY pulse          : SCK
    serial program mode      : yes
    parallel program mode     : yes
    Timeout            : 200
    StabDelay           : 100
    CmdexeDelay          : 25
    SyncLoops           : 32
    ByteDelay           : 0
    PollIndex           : 3
    PollValue           : 0x53
...
    Programmer Type : Arduino
    Description   : Arduino
avrdude: Send: A [41] . [80] Â [20]
avrdude: Recv: . [14]
avrdude: Recv: . [02]
avrdude: Recv: . [10]
avrdude: Send: A [41] . [81] Â [20]
avrdude: Recv: . [14]
avrdude: Recv: . [01]
avrdude: Recv: . [10]
avrdude: Send: A [41] . [82] Â [20]
avrdude: Recv: . [14]
avrdude: Recv: . [10]
avrdude: Recv: . [10]
avrdude: Send: A [41] . [98] Â [20]
avrdude: Recv: . [14]
avrdude: Recv: . [03]
avrdude: Recv: . [10]
    Hardware Version: 2
    Firmware Version: 1.16
avrdude: Send: A [41] . [84] Â [20]
avrdude: Recv: . [14]
avrdude: Recv: . [00]
avrdude: Recv: . [10]
avrdude: Send: A [41] . [85] Â [20]
avrdude: Recv: . [14]
avrdude: Recv: . [00]
avrdude: Recv: . [10]
avrdude: Send: A [41] . [86] Â [20]
avrdude: Recv: . [14]
avrdude: Recv: . [00]
avrdude: Recv: . [10]
avrdude: Send: A [41] . [87] Â [20]
avrdude: Recv: . [14]
avrdude: Recv: . [00]
avrdude: Recv: . [10]
avrdude: Send: A [41] . [89] Â [20]
avrdude: Recv: . [14]
avrdude: Recv: . [00]
avrdude: Recv: . [10]
    Vtarget     : 0.0 V
    Varef      : 0.0 V
    Oscillator    : Off
    SCK period    : 0.1 us
avrdude: Send: A [41] . [81] Â [20]
avrdude: Recv: . [14]
avrdude: Recv: . [01]
avrdude: Recv: . [10]
avrdude: Send: A [41] . [82] Â [20]
avrdude: Recv: . [14]
avrdude: Recv: . [10]
avrdude: Recv: . [10]
avrdude: Send: B [42] . [86] . [00] . [00] . [01] . [01] . [01] . [01] . [03] . [ff] . [ff] . [ff] . [ff] . [00] . [80] . [04] . [00] . [00] . [00] . [80] . [00] Â [20]
avrdude: Recv: . [14]
avrdude: Recv: . [10]
avrdude: Send: E [45] . [05] . [04] . [d7] . [c2] . [00] Â [20]
avrdude: Recv: . [14]
avrdude: Recv: . [10]
avrdude: Send: P [50] Â [20]
avrdude: Recv: . [14]
avrdude: Recv: . [10]
avrdude: AVR device initialized and ready to accept instructions
Reading | avrdude: Send: u [75] Â [20]
avrdude: Recv: . [14] . [1e] . [95] . [0f] . [10]
################################################## | 100% 0.01s
avrdude: Device signature = 0x1e950f
avrdude: Send: V [56] . [a0] . [03] . [fc] . [00] Â [20]
avrdude: Recv: . [14]
avrdude: Recv: . [00]
avrdude: Recv: . [10]
avrdude: Send: V [56] . [a0] . [03] . [fd] . [00] Â [20]
avrdude: Recv: . [14]
avrdude: Recv: . [00]
avrdude: Recv: . [10]
avrdude: Send: V [56] . [a0] . [03] . [fe] . [00] Â [20]
avrdude: Recv: . [14]
avrdude: Recv: . [00]
avrdude: Recv: . [10]
avrdude: Send: V [56] . [a0] . [03] . [ff] . [00] Â [20]
avrdude: Recv: . [14]
avrdude: Recv: . [00]
avrdude: Recv: . [10]
avrdude: reading input file "/tmp/build1252157735055366361.tmp/LightBrick.cpp.hex"
avrdude: writing flash (17602 bytes):
followed by many lines of output of bytes being sent to the arduino's flash memory, with intermittent receives, and ending with something like this:
avrdude: Send: t [74] . [00] . [80] F [46] Â [20]
avrdude: Recv: . [14]
avrdude: Recv: . [80] . [93] ? [3f] . [05] . [0e] . [94] . [be] . [18] q [71] . [c6] / [2f] p [70] # [23] 0 [30] . [09] . [f0] . [a2] . [c7] . [88] . [e0] . [80] . [93] ? [3f] . [05] . [0e] . [94] . [be] . [18] & [26] . [c6] . [85] 0 [30] . [19] . [f5] . [e0] . [91] @ [40] . [05] . [f0] . [91] A [41] . [05] . [84] . [81] . [95] . [81] . [89] + [2b] . [09] . [f4] . [91] . [c7] . [10] . [92] E [45] . [05] . [10] . [92] D [44] . [05] . [c9] . [01] . [0c] . [97] . [90] . [93] C [43] . [05] . [80] . [93] B [42] . [05] . [90] . [93] : [3a] . [05] . [80] . [93] 9 [39] . [05] . [10] . [92] 8 [38] . [07] . [10] . [92] 7 [37] . [07] . [10] . [92] 8 [38] . [05] . [10] . [92] 7 [37] . [05] . [88] . [e0] . [80] . [93] ? [3f] . [05] . [aa] . [c1] . [80] . [91] k [6b] . [05] . [90] . [91] l [6c] . [05] . [01] . [96] . [90] . [93] l [6c] . [05] . [80] . [93] k [6b] . [05] . [e9] . [01] . [a8] . [97] . [80] . [91]
avrdude: Recv: . [10]
avrdude: Send: U [55] @ [40] . [09] Â [20]
avrdude: Recv: . [14]
avrdude: Recv: . [10]
avrdude: Send: t [74] . [00] . [80] F [46] Â [20]
avrdude: Recv: . [14]
avrdude: ser_recv(): programmer is not responding
avrdude: stk500_recv(): programmer is not responding
the timing of which correlates with my "on" LED turning back on.
Does this sound like the "resetting too soon" issue Grumpy_Mike suggested to everyone else as well?