Automate Custom property tags

Can a custom property tag be assigned to a computer automatically when its registered in BigFix?

Yeah, if you set a policy action with relevance to look for it being there and if its not then apply it or you can do it with the client Config file at point of installation.

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I have custom property set for several systems in my environment. When I ran an analysis on the custom property field only 29 of 35 were seen. How can I determine why the 6 systems did not show up in the analysis. Doing this prior to creating automatic groups

You can check the client logs.

Also, check the relevance in the analysis and check the relevance in the site subscription (e.g. make sure they are subscribed to the site where the analysis lives)