When attempting to connect my Thumby to the IDE, I can connect it using "Connect Thumby" button and the Chrome popup shows the serials ports but then nothing happens after that and I recieve this error in the JavaScript Console:

Serial supported in this browser! main.js:765
Restored layout from previous state editor_wrapper.js:415
INIT CODE VIEWER repl.js:796
Trying auto connect... repl.js:802
Auto connected! repl.js:781
Opening port failed, is another application accessing this device/port? main.js:781

Any ideas?

As the error implies, it is likely that something else is accessing the device and taking over the port before the IDE can.

Make sure only one IDE page is open in one browser. Also try restarting your computer.