In addition to those that have written, I can offer the following:
-If you cleaned the flight tube, the magnet might be off kilter by a tiny margin. It is possible it needs to be put back into its exact previous position, which is a very touchy operation with a rubber mallet. This is only if the peaks aren't lined up with one another.
-If you wanted to be sure it's not the electronics or source cleaning: Run a scan of intensity vs time for several hours (preferably overnight) with your standard gas. In the morning, blow up the plot so you can see the resolution of your prominent cup during the scan time. If there's any noise or bad resolution (steps, negative spikes, etc) you may have leakage current across your ceramics. If you're sure the source isn't an issue, and the bad peak shape is on all the cups, look into the ion source control board next. Hope this helps.