There are some bugs documented and fixed in SR6 and SR7 related to sorting. However, I'm not sure if I understand your issue: you build a QVW file and sort a column in a chart. Then you publish this app to the Server and what you see is different to what you stored?
Are you using section access?
Are you using calculated dimensions or sorting by expression?
Is that a straight table or a pivot table?
Are you able to manually sort the chart using the double click in the label of the column in the Ajax client?
Using section access means that some records will be removed depending on the user logging in, therefore the sorting should be actually different depending on the user. This is the behavior I'd expect.
Sorting with calculated dimensions is not a good idea (not to mention performance issues): take a look at bug #66210 fixed in 11.20 SR6 and its corresponding text in the Reference Manual sectino 50.5 Chart Properties, Dimension Limits.