Early versions (1994-1998) of the 2nd generation board were sent out with tall header pins for all 3 2x13 pin headers. However, the header used to connect an RBUF-Term (J4) only needs to be standard height (a normal height header is sent for this now) If the RBUF-Term cable is installed, it sometimes is too tall to allow for the proper installation of daughterboards.
If your board has tall pins you can try a few things
1) If you have a steady hand and a good eye, you can trim the pins on J4 in half. Ensure you don't bend them and keep the cuts level
2) Some RBUF-Term cables have a second clip which holds the ribbon cable down as it loops back over the connector. Try removing this. RBUF-Term cables currently shipping are wired without this strain relief allowing for easy installation of motherboards
3) If you'd rather leave everything alone, contact Creative Control Concepts at support@cc-concepts.com for an extra pair of header sockets to raise the daughterbaord stack up
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Home Automation FAQ : 
My header pins are too short to mount my daughterboard. Now What?