I made a lot of progress...
As I mentioned, I had modified the SoftwareSerial library under Arduino v0.22 to work with what at the time we called the Sanguino which was based on the 644P, and has the same pin out as the 1284P.
maniacBug had released his 1284P support, and I had asked him to do a version that matched the pin out nomenclature of the AVR Developers 1284P support, which he did. So i don;t know if the issue I had related to the Maniacbug 1284P or the AVR Dvelopers 1284P, but I'll get to the bottom of it.
In case anyone is interested, the changes I made are in pins_arduino.h. I have not checked yet to make sure i didn't break anything else. I suspect I probably did, but we'll see.
Here is the original:
#define digitalPinToPCICR(p) (((p) >= 0 && (p) < NUM_DIGITAL_PINS) ? (&PCICR) : ((uint8_t *)0))
#define digitalPinToPCICRbit(p) (((p) <= 7) ? 1 : (((p) <= 15) ? 3 : (((p) <= 23) ? 2 : 0)))
#define digitalPinToPCMSK(p) (((p) <= 7) ? (&PCMSK2) : (((p) <= 13) ? (&PCMSK0) : (((p) <= 21) ? (&PCMSK1) : ((uint8_t *)0))))
#define digitalPinToPCMSKbit(p) ((p) % 8)
Here are my changes:
#define digitalPinToPCICR(p) (((p) >= 0 && (p) <= 31) ? (&PCICR) : ((uint8_t *)0))
#define digitalPinToPCICRbit(p) (((p) <= 7) ? 1 : (((p) <= 15) ? 3 : (((p) <= 23) ? 2 : 0)))
#define digitalPinToPCMSK(p) (((p) <= 7) ? (&PCMSK1) : (((p) <= 15) ? (&PCMSK3) : (((p) <= 23) ? (&PCMSK2) : (((p) <= 31) ? (&PCMSK0) : ((uint8_t *)0)))))
#define digitalPinToPCMSKbit(p) (((p) <= 7) ? (p) : (((p) <= 15) ? ((p) - 8) : (((p) <= 23) ? ((p) - 16) : ((p) - 24))))