It's most likely that some module folder are nesting other folders with the module files withing them. You must ensure that a module folder contains ONLY module files, not another top folder holding the module file contents.

Also ensure that the module name is correct. Most modules only allow the originla unchanged name to be used. If in doubt check the xoops_version.php file. It will have something like this:

$modversion['dirname'] = "mylinks";

mylinks is the only name you can call this module.

Some modules allow for name changes, but confer with the instructions for this.