i use a paper towel too but dont have this problem, usually starts to skim in 15 to 30 minutes.
are you adjusting the air intake cause if it explodes and floods, you have open up the air intake that would cause this.
usually when i clean the skimmer, it leave it running. grab a old 5 gal salt buckets, pull off the cup, stick in it the bucket, grab a paper towel, clean the riser, throw dirty towel in bucket. wash the cup with plain old water, place cup back on skimmer. i dont mess around with air intake or gate valve adjustments cause its set right on the dial.
ever since i upgraded to a eheim 1262, i get 300% more skimmate. in three days, i have the three times the amount of skimmate. i havent clean the cup every other day cause i wanted to see and measure what i get per day. i am very impressed with the results of upgrading from a mag 5 to an eheim 1262. pics later today