You probably have a .BIN file that is not part of a CUE/BIN image... it's only the binary file of the tool you want to burn.

You should check if it's a scrambled or unscrambled binary file, then build a .ISO with the YOURTOOL.BIN inside it, and then use BIN2BOOT YOUR.ISO /nohack

when it asks to create a IP.BIN answer yes, and point it to YOURTOOL.BIN

if this is a bit confusing, try searching for a .SBI version of the tool you want to burn, and then use Dream Inducer (selfboot inducer)