Eric, did you ever find a fix for this? We're experiencing the same behavior. Running a filter on the same mapservice works fine in our ArcGIS Online account, but when we try it in Portal nothing updates on the map. The view of that layer becomes a static image, just as you showed on your original post (e.g. it becomes pixelated when you zoom in on it and panning off of it shows that it is 'stuck' in the original extent). Other layers continue to refresh correctly, so the strange behavior is limited to the layer on which we tried to filter.
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