The little round plasitc spacer gets worn over time. (between the control panel and joytop) This may be what causing the longer travel. To fix this... dismount the joy, and flip the spacer over.
However... you may just want to live with them untill it gets really bad and dosnt touch the micros correctly.
Spacers usually last a long time... but heavy handed play can cause quicker wear. If you are agressive in your play... you may want to get supers instead.
Spacers are pretty cheap tho... so its not a huge deal.