Incorrect taxes

I notice that in BSI tax factory 9.0 the taxes are not getting calculated correctly for states which are not having any kind of reciprocity between them. When two states do not have any kind of reciprocity between them the taxes should be calculated for both the states but the employees in Tax factory 9.0 are not getting taxed for both the states. It is only when i set up the nexus indicator it is working correctly. I though that the nexus indicator is only used for the states which are having reciprocity between them and not for others. So now does this mean that i need to setup the nexus indicator for all the states? Please advise?