Also on Splunk 5.0.2, just in flashtimeline or charting views. "Span" is likely a time range you're running the search over - the message would not pop up or all time searches or real time searches - but any other timespan had this message appear.
I tested and despite the message saying it has no effect, it certainly does have an effect:
... | timechart minspan=30s count by ... makes 30 second buckets on a
Last 15 Minutes search. However,
... | timechart minspan=5s count by ... makes 10-second buckets. Case 114952 filed.