have you recently changed the amounts of DNA in your sequencing reaction or do you load in a formamide based dye ??
If it isn't s a spent array or one in need of a nitric acid wash - you say the array has been changed - then I have seen the phenomenon you describe relating to the above. In particular, over loading your sequencing reaction reaction with too much DNA may culminate in excessively wide peaks, although usually from the outset, and 'spent' formamide, which contains ionic species like formates can lead to the premature breakdown in resolution .
One more thing: Having changed the array, did you run standards like pGEM to check the quality of respective capillaries ??
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