It may be very hard to debug this problem (pardon the pun) over a mailing list. Just way to many factors that could influence what's going wrong, but let's try.
You say you have the debugger running, and you say "started" (did you mean "stopped"?) on a line. That's a great head start. Many can't even get to there due to config issues (getting the server-side config right, getting the RDS and Server properties in CFB right, getting the project properties to point to that, getting the debug configuration properties right, starting a debug session, etc.). So you're on the right track.
So when you say it "5 lines in", do you mean you're doing step over or into on each? What is the last line where things work? And what happens?
Could it be simply that the logic flow at that point is finished in the app.cfc? If so, then you'd need to have set a breakpoint in whatever next point you want to stop at. Does that help?
I apprecaite you taking the time out of your schedule to help out.
After a few reboots and restarts of CFB it appears to be working. Which is odd since I have not changed a setting at all on the program.
I will watch it closely and see if anything else happens. It does appear to be a little slower than Fusion Debug but, its working for now.
Thanks for stopping by