I just did a brief test and I don't see this behavior when changing the user under which the service runs. But of course my test user account probably has more or different rights than what they use.

Note that in 20.0 we changed how certain instructions are passed from the administrator into the webapp server (to improve the responsiveness of the administrator and to allow the server to be a bit smarter in which thread performs those operations). Those operations are now passed via the registry (Computer\HKEY_LOCAL_MACHINE\SOFTWARE\Data Access Worldwide\DataFlex\20.0\WebApp Server Commands). Normally this should be empty, do you see entries there? Can you check if the user running the service has sufficient rights on this key?