Situations in which a configuration is excluded from being built by the combination filter are handled in a very confusing way in Matrix Reloaded plugin. The problems are the following:

1. Configuration changes are not detected properly - the warning on the configuration selection page is always shown, even when there was no change in the configuration. IMHO the message provides very little value anyway and I would suggest it is not displayed at all.
2. Combination filter is not visible in any way in the matrix, but it is applied (as it should be). As a result, you select a set of configurations to reload, but only a subset of those is actually run, getting filtered out by the combination filter afterwards. It would be very useful if those configurations were highlighted on the main page in some way. Such highlighting could replace the configuration change warning. Obviously we cannot detect them reliably if the filter itself contains build parameters, but filtering out other cases would be very useful anyway.