Sorry for what I am going to say, but without further work, I think you will not be able to use both libraries at the same time.
It you are sooooooo lucky, maybe you can. But at first look, no.
What is happening here is that both libraries use Timer/Counter 2 to throw an interrupt: Timer/Counter 2 Overflow.
The name of the interrupts are in \hardware\tools\avr\avr\include\avr\iomx8.h
In that file you will find:
#define TIMER2_OVF_vect _VECTOR(9)
What is incredible is that it works with and undefined define TIMER2_OVF_irvect.
So, what you did is "disconnect" the IR interrupt service.
1.- If both modules use the same frequency (barely possible), just converting one of the service in one module to a function, and calling that function from the other module's interrupt service will be enought.
2.- Reprogram one of the modules to use Timer/Counter 1 or Timer/Counter 0.
3.- Do the 1 solution, using the highest frequency and control by software the freq of the slower module (just a counter to know when to call the function, for example).