While debugging my project in Eclipse, it will (repeatably, at the same point in the code) pause execution as if it's reached a breakpoint. No exceptions are thrown, the project has no breakpoints, and if I hit resume, it carries on without a problem.
What could be causing this behaviour?
Your code and the binaries that you are debugging are not in sync.
Try creating a break point and then getting rid of all breakpoints and see if it still happens.
Create a fresh workspace and import your project to this newly created workspace. The problem should be gone, especially if the problem was caused by corrupt workspace metadata.
it could also be waiting for user input, or a particular action to take place so it can continue.
The Eclipse debugger pauses if the code throws an exception - at least it does for me (maybe this can be toggled). Just un-pause the thread and you'll most likely see a stacktrace being printed to STDERR.