Problem running file under windows schedule

I have a set up a small FMP database that runs on a server that hosts a web-based application (non-FileMaker) created by a another company. The purpose of the FMP database to simply to trigger two scripts - one that imports data from a file on that server into a database being hosted on Filemaker Server, and one that exports another datafile from a second database hosted on Filemaker Server, to be picked up later by this third-party application. The file simply calls the two scripts and then closes. It takes about 2 minutes to run. FileMaker server is hosted on a separate Server in close proximity on the network.

The file is triggered by a scheduled task in windows. Since we set it up with FileMaker Pro 8.5 about 8 months ago, it has work flawlessly, kicking in twice a day, importing and exporting as required as required.

My problem is that I recently asked our IT people to upgrade the FileMaker client software to 9.0v3, so that it is the same as all other users of our systems. Under version 9 however, the scheduled task will only run if I remain logged in as a user on the computer on which the scheduled task is to run. If I log off, so that the task should run without the user needing to be logged in, it fails to run. We have tried everything (setting up new scheduled tasks, logging in as sifferent users), but we can not seem to get it the scheduled task to work as it did with 8.5. I have just had the IT guys roll-back the software to 8.5 and it works fine again.

Is anyone aware of any change to FileMaker Pro that would be causing this problem, and it there is any way around it, short of using an older version of the software?