Answer
After installing ArcIMS 9.3.1 (upgrade or new install), the following Windows services still show version 9.3:
▪ ArcIMS Application Server
▪ ArcIMS Monitor
▪ ArcIMS Tasker
This is known issue. The post installation creates these services, and these processes were not updated in 9.3.1.
To verify that ArcIMS is at version 9.3.1, run the ArcIMS Diagnostics from Start > Programs > ArcGIS > ArcIMS > Diagnostics.
If the tests come back as successful, they should show version 9.3.1.
IMS v9.3.1
Build_Number=2095.1916
Version=9.3.1
Test successful