It looks like there is some resource which doesn't get unloaded when you quit your application.
Double check if you destroy the PBDom_Builder, and remember to destroy external resources manually - do not trust the in-built garbage collection.
When you load a DLL (and PBX are DLL under the hood) from the compiled IDE, the DLL gets loaded in your application's process. Once you quit the application, the DLL gets scrapped with your process.
When you run your application from the IDE, Powerbuilder loads the DLL in the PB115.EXE process.
If something goes wrong, the IDE process gets unstable and the second time you fire your application, it may crash.