The QBSDK does not like Windows services (or IIS for that matter) working with the QBW file. They have a work around, but it's not pretty, and from my experience, not overly reliable.
It requires a COM component called QBXMLRP2e.exe
the developer guide has some information on it, but googling will provide better results.
I'd supply some code that I wrote when trying to use this, but a) it's abandoned and I don't know exactly where it is, and b) it didn't work right in the first place so I don't want to send you down the wrong track.
Sorry I couldn't have been more help.