I am obviously unaware of all the moving parts you have integrated into this whole thing. It sounds like an architecture without an architect. If you are ever going to have clean solutions to these integration issues, somebody has to be looking at how to make all the pieces work and play well together.
A much more effective way than trying to automate filling in prompt values in regularly scheduled reports is to have the values live in one or more parameter tables in the database. The report SQL then pulls the parameters from the tables directly and you don't have all this mess and you can stop trying to push on a rope.
You can still use a Java application to fire off reports with special sets of parameters; you just have it create a unique ID that identifies the particular parameter set, stuff the parameters in the table(s) with that id, then schedule the report in BCA filling in a single prompt, the parameter_set_id. For regularly scheduled daily reports, the parameter sets would be pre-built in nightly batch jobs and the reports schedule with a default or hard coded parameter_set_id.
It sounds as if your site has been trying to take un-modified user-written reports and automate them. While it is theoretically possible (you are doing it) it is kind of unrealistic. The automated reports should be setup to be automated and not simply duplicates of interactive reports. At least that is what I have found works cleanest and most efficiently with BO.
Regards,
Bill
