I compiled this sketch fine:
ISR(TIMER2_COMPA_vect) {
PIND = 0xf0;
}
void setup() {}
void loop() {}
on both 1.0.1 and the newest github version (commit 222d51e3831d77f60ae6ce1f3d037b0febb0c717) with avr-gcc 4.7.1 and avr-libc 1.8.0
What "problems" are you having?