Since you have the source code for VFP6, I would suggest looking into
SYS(2335,0)
Sys 2335 is used to identify if the program is running in an "unattended" mode, any such popup dialog boxes will throw an error and prevent an actual "hit" ok/cancel/whatever button to continue. This includes popup window prompting user to pick a table.
I'm not positive of when it was made available as I had limited use of it. Like you, when dealing with a COM server under IIS and obviously nobody there to respond.