AVR-Chat

>
>I guess there needs to be a eeprom_busy flag so nothing else tries to
>use the eeprom while the ISR is busy.

There is an EEPROM ready ISR, so you could just do it from there.
If the EE is ready, then you can start another write.
You have to "kick start it" by doing the first write outside the int 
though, or you could do a dummy read.