I believed I solved it... at least for my installation.
I originally I installed the Arduino 1.6.6 IDE about a year ago when my Mac was running and older version of OSX (10.9?). No problems. About six months ago I added RFduino support including the FTDI VCP driver as recommend by RFdunio - again, no problems.
When I upgraded to El Capitan that's when my FTDI issues arose. Turns out if you RTFM you will find answers - in this case the fine manual
in question is the FTDI Mac Drivers Installation Guide:http://www.ftdichip.com/Support/Documents/AppNotes/AN_134_FTDI_Drivers_Installation_Guide_for_MAC_OSX.pdf
In Section 3.2 of the guide, they state "Starting with 10.11 (El Capitan), Apple's own driver seems to be sufficiently comprehensive that many customers will not need to install FTDI's own VCP". This is all true, but if you upgraded your OS like me, it turns out that the FTDI VCP driver I installed for OSX 10.9 was still present even after the El Capitan upgrade.
The solution: Uninstall the FTDI VCP driver so that OSX will use the default Apple driver. To uninstall, follow the instructions in Section 4.2 of the FTDI guide. You may need root permissions to do this - Google that if you don't already have this.
Hope this helps others.
To the RFdunio team: Please update your installation docs / Github readme accordingly to prevent new El Capitan users from installing the FTDI VCP driver.