Removing inactive items from Matrix

Here is the situation. We have 4 store locations all running RMS and 1 computer running HQ v 2.0.0157. I've set up a number of matrixes through HQ and uploaded them to all of the store locations. I now have some items that I have turned inactive in HQ because we are no longer selling them. Already i have gone through and physically removed all of those items from the matrix in HQ and have run worksheet 250 with all of those items to the store locations. After the WS has been run, the items are in fact inactive in RMS but they still appear in the matrix. Is there anything I'm missing, is this a bug, a missing feature, etc?

In comparison I have gone through the same process in the past with adding and removing items from assemblies in the same fashion and have had no issues. Any ideas?