When calling selenium-server like this:

  java -jar selenium-server.jar -htmlSuite *firefox http://localhost:8080 "M:\Master\STC.html" "M:\results.html",

the given baseUrl is not used directly but "/selenium-server/tests" is added automatically. So a test that should, for example, open "index.html" (relative path!) fails with error 404 because the browser tries to open the URL "http://localhost:8080/selenium-server/tests/index.html", which does not exist.
(/index.html works because of the leading slash; but then we have a number of test suites that use relative URLs and they work in Selenium IDE.)

When I manually "correct" the baseUrl parameter in the browser window and open that URL, everything works as expected.

The <selenese ...> ant task shows the same problem.