I am sure this could not be it, but I did it once...do you have more than one Moodle database on the server? I once caught myself working/making changes in the wrong database on a server that had five different Moodle installations on it. I kept wondering why my changes were not making any difference till I realized what I was doing.
Another possibility - I had a similar problem once. I fixed it by changing the version number in the module I wanted to install so that its version was one digit higher than the one I wanted to replace. Moodle then would perform the "upgrade" to the "new" version. Just had to remember and redo it it when I updated versions of Moodle later until I did a new from scracth install.
Hope this helps.