There may be different weight matrices describing the same site. One reason is that those matrices are based on different training datasets originating from independent publications. Usually, those matrices belong to the same matrix family and can be used together. Both threshold have to be reached for a matrix match. The occurence of a single transcription factor binding site found by GEMS Launcher does not give you any hint that this site may also be functional.
Functionality is determined by the sequence context.
If a binding site is part of a framework of two or more sites there is a stronger evidence that the individual sites may be functional. Therefore, identification of single matrix matches is usually only a first step in promoter analysis , the subsequent aim will be the identification of more complex promoter models . Comparative sequence analysis is based on the hypothesis that functional sites are preserved during evolution and therefore higher conserved than the sequence context. A suitable training dataset may contain orthologous or homologous promoters or, for instance, promoters from co-regulated genes found by expression array analysis. Usually, promoter models are much more specific than single elements like transcription factor binding sites.