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I am using Creo Parametric Release 9.0 and Datecode9.0.0.0
ProMdlModificationVerify -> API Giving Modified Flag always True for particular Sub-Assembly. Even after Save and reopen . Since it is a Customer part we are unable to share the Assembly with you . If needed we can connect for Remote debugging .
PTC R&D introduced new API named as ProMdlVisibleModificationVerify() in Creo 7.0.12.0, Creo 8.0.10.0, Creo 9.0.6.0 and Creo 10.0.2.0 to verify model modification status correctly.
As a work around, you can use a notifier on open, save the model stamp and compare this if you want to check for modifications.