What column and eluent are you using? Which autosampler, if any, do you use? I can suggest some experiments to isolate the problem when I know more about your setup.
The operator's manuals that come on the Dionex CD will describe all the recommended cleaning and maintenance procedures. There is too much to list here.
Autosampler is simply AS. Columns:  guard (AG11) and analytical (AS11) and the eleunt is KOH ( Eleunt catridge) + D.I water( Eleunt) . KOH is given by the manufacturer which has a 44 % life remaining and D.I water is from our lab which we generally change everyday.
Usually i  read the operators manual. can u exactly tell me where in the manuals i can get the cleaning and maintenance procedure to isolate this problem? 
Thanks for your time.