Your sketch looks good, I noticed during my test that isPresent(..) method works, whatever IRQ is. Because there is no transmit/receive while trying to detect module, So I'm suspecting a chip select problem, but,
You said you connected RFM12B CS to D18, just to be sure, this is connected to PC2 Pin of Atmega 1284p right ? and you're using Felix's Mega Arduino IDE board and source ?
The pin definition is tweaked by Felix are :
// ATMEL ATMEGA644P/1284P
//
// +---\/---+
// PCINT8/(D0 ) PB0 1| |40 PA0 (A0 / D24)/PCINT0
// PCINT9/(D1 ) PB1 2| |39 PA1 (A1 / D25)/PCINT1
// PCINT10/INT2 (D2 ) PB2 3| |38 PA2 (A2 / D26)/PCINT2
// PCINT11/OC0A (D3 ) PB3 4|~ |37 PA3 (A3 / D27)/PCINT3
// PCINT12/0C0B/SS (D4 ) PB4 5|~ |36 PA4 (A4 / D28)/PCINT4
// PCINT13/MOSI (D5 ) PB5 6| |35 PA5 (A5 / D29)/PCINT5
// PCINT14/OC3A/MISO (D6 ) PB6 7|~* |34 PA6 (A6 / D30)/PCINT6
// PCINT15/OC3B/SCK (D7 ) PB7 8|~* |33 PA7 (A7 / D31)/PCINT7
// RST 9| |32 AREF
// VCC 10| |31 GND
// GND 11| |30 AVCC
// XTAL2 12| |29 PC7 (D23) TOSC2/PCINT23
// XTAL1 13| |28 PC6 (D22) TOSC1/PCINT22
// PCINT24/RX0 (D8 ) PD0 14| |27 PC5 (D21) TDI/PCINT21
// PCINT25/TX0 (D9 ) PD1 15| |26 PC4 (D20) TDO/PCINT20
// PCINT26/INT0/RX1 (D10) PD2 16| |25 PC3 (D19) TMS/PCINT19
// PCINT27/INT1/TX1 (D11) PD3 17| |24 PC2 (D18) TCK/PCINT18
// PCINT28/OC1B (D12) PD4 18|~ |23 PC1 (D17) SDA/PCINT17
// PCINT29/OC1A (D13) PD5 19|~ |22 PC0 (D16) SCL/PCINT16
// PCINT30/OC2B (D14) PD6 20|~ ~|21 PD7 (D15) OC2A/PCINT31
// +--------+
//
By the way I just saw a bug for D2 as IRQ, I fixed it and just updated the library, could you retry with IRQ D2 (which should not solve if the problem is coming from CS 18 pin)
So last test could be, if it's possible for you to change CS pin, just to see and connect it do D4 (PB4 of atmel)
#define RFM_CS_PIN SS // RFM12B Chip Select Pin
#define RFM_IRQ_PIN 2 // RFM12B IRQ Pin )
I think I'm definitely need a 1284p board to investigate on this issue, because I'm using the lib on several different 328p boards, with D2/D3 as IRQ and D10/D5 as CS without any problem.
Let me know it it's better like that