So the the first problem is that you have less than 20 data points per Module which leads (with the cut-off set) that the test is not performed because it may be difficult to trust.
The identifier that will be shown in the result heatmap depends on the identifiers in the mapping file: If you the file maps Uniport Ids to KEGG ids (e.g. hsa:012212) these Kegg Ids will be shown in the heatmap. Note that there should be an annotation file that has been download with the .tcm file which contains the KEGG pathway names so you can add it as a text label.
You other file seems to map directly to the pathway names, which seems to work fine also. What is weird is that the results differ so much between the two mappings! Could you load the pathway names in the heatmap with only hsa-identifiers and check if the results coincide?
Also to check if the modules are the same between the two annotation, select one or two pathwyas and check if the annotated UNIprot Ids coincide?