If you have one or more plugins disabled in builder toolbar (e.g., commerce or other), there can be 2 reasons for this:
You have this plugin disabled per plans configuration. To check this:
open Site.pro licenses page;
click on your brand to open it;
go to item "Edit Plans";
check what plugins you have disabled for each builder plan and enable some of them if needed.
You specified wrong hosting plan names in field "Relate with these hosting plans"; as a result, the wrong builder plan is loaded for the customer. In this case check real hosting plan names from your end and fix their values on Site.pro if needed.