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Try setting the debugger to 'Step into' on startup. That should at least give a clue to whether your setup is right.
Tools|Preferences|Debugger|Start Debugging Option | Step Into.
Another potential cause is that none of your breakpoints is on a code line. I don't remember when it occured but there was a change in how it handled line numbering and the extra 'Create or replace' line at the top of the buffer.
There's a pretty bad bug in 3.2 for the debugger. Line numbers are off by 1 - so setting a breakpoint on line X is being seen by SQLDev as being on line X+1
We'll have this fixed ASAP.
It may NOT be related to your issue, but it's likely involved.
To confirm, download v3.1 and try it there. If it's not working there as well, then we have a different issue.