Can you give us an example? I'm having exactly the same problem with an AT90CAN in MPLABX. I tried this...
ISR(TIM1_CAPT)
{
Period++; // arbitrary test code, just to give it something to build
}
and it moaned...
"/Applications/microchip/xc8/v2.05/bin/xc8-cc" -mcpu=AT90CAN32 -c -x c -D__AT90CAN32__ -Wl,--gc-sections -O0 -ffunction-sections -fdata-sections -fpack-struct -fshort-enums -funsigned-char -funsigned-bitfields -I"../../../../../../../Applications/microchip/xc8/v2.05/avr/avr/include/avr" -Wall -DXPRJ_default=default -gdwarf-3 -MD -MP -MF "build/default/production/TranslateSensors.o.d" -MT "build/default/production/TranslateSensors.o.d" -MT build/default/production/TranslateSensors.o -o build/default/production/TranslateSensors.o TranslateSensors.c
TranslateSensors.c: In function 'TIM1_CAPT':
In file included from TranslateSensors.c:15:0:
TranslateSensors.c:76:5: warning: 'TIM1_CAPT' appears to be a misspelled signal handler, missing __vector prefix [-Wmisspelled-isr]
ISR(TIM1_CAPT)
^