Inconsistencies when using ConfigSets and calling rtwbuild

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Hello!
I want to generate code using a complex model. The model is using other referenced models. As I want to compare the effect of different settings (ConfigSet paramters) in code generation, build and during runtime I have started using ConfigSet references.
That means the model(s) are using paramters based on workspace variables of type ConfigSet. I am loading a .mat file which includes all ConfigSets for all models. Then I want to modify specific settings, 'ProdHWDeviceType' to 'Texas Instruments->C6000'. This is done automatically by overwriting the workspace variables. Then I call rtwbuild.
Sometimes there seems to be an inconsistency, as the generated rtw files lists 'ProdHWDeviceType' as "Intel->x86-64 (Windows64)".
Any hints of what I am doing wrong in the process?
Thank you,
Matthias

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