Usually missing button in editor is caused by cache - you can see it also if you make changes to files of your theme and don't refresh your browser (or clean cache or file history of your browser). In htmlarea cache lifetime is 1800 seconds = 30 minutes, for files of theme it is 10 minutes in moodle 1.9 and 30 minutes in moodle 2.0. So if you have used your editor just before making changes you will need to refresh browser after changes to see the effect.
Sometimes people unzip files to wrong folder (sub folder or parent folder) or files may have wrong permissions - a simple filemap /file tree or list of version changes in readme file could be useful. I usually test files first in a local PC (Windows package of moodle / Windows Vista) and compare the files and folders with Winmerge http://winmerge.org/about/screenshots/ - possible errors can be usually found from server (apache) error log or for example FF error console or in IE8 with developer tools...or by setting debugging to ALL from administration menu of moodle if the reason is in moodle itself. If local install looks ok I usually upload the files to my Debian Lenny test server and check again possible errors on linux environment.
It should not matter if you leave the old files uninstalled because new files are using new paths - unless your browser is still using the old files from cache and finds them...