If you could 1) show what type of graph you are attempting and 2) some example data you may have a lot better chance on getting a solution.
Depending on what's going on I might try setting at thicker axis line, effectively "hiding" the zero height bar. Or pre-summarizing the data to identify those X axis value cases and set an attribute data set for the border/fill that are 100% transparent.
Or possibly delve into GTL