This is an answer to anyone having problems getting a program to appear in the Blackberry simulator or problems generating a COD file.
I have been programming in JAVA using the Eclipse IDE and my program was working fine in the BB simulator. After creating a new package and adding more class files to my project, I noticed that my changes were not being reflected in the simulator. After countless hours trying to solve the problem (cleaning, running clean.bat, deleting cod files, creating a new workspace, etc. - nothing worked) I just discovered an answer on a forum that solved my problem:
I had 116 files in my project. I deleted two packages to get the number of classes under 100 and, voila, a new COD file was generated and my changes are reflected now in the Blackberry simulator. This is obviously a bug that RIM needs to address. I wasted days debugging this until I found a solution.
Hoping this helps someone with similar problems.