Hi, @jimmy623,
Recently, the last version of S32K3 Toolbox was released, namely version 1.5.0. Try an installation of this version and check if you still have problems using the custom linker.
It is worth mentioning instead that if the intention is to use the S32K3 toolbox together with the BMS toolbox, which work together, they are functional for the moment only in version 1.4.0 of the S32K3 toolbox.
Let us know if your problem persists.
Regards,
Dragos