I don't know the details, but its a bug triggered when an interrupt routine calls another routine. If interrupt routine does all the work itself rather than calling a subroutine, I suspect that might cure things - so you'd need to re-write a copy of SoftwareSerial to do things this way.
The underlying problem is probably that the calling convention used in avr-gcc is not the same as that used by the hardware interrupt-handling.
It might be worth investigating which version of avr-gcc you have and what the current version is - try upgrading to that (but be prepared to back-out again!). I know my (elderly) ubuntu install is using v. 4.3.5, if you post the complete SoftwareSerial mod you have some of us could test if it compiles on their installs.