I agree with SB_James, something isn't right.
CW is correct in stating that some style slides drop in place a little (designed to do so) upon full extension, but the top horizontal dual 'wiper seal' should still be making contact the full length of the slide roof EPDM when fully extended.
My slide roof fully extended looks like this:
To compensate for the slight slide drop my slide roof has an approx. 6"-8" wide by approx. 1/2"-3/4" high styrofoam riser located under the slide EPDM roofing material that insures that the wipers maintain contact with slide fully extended. I have a Lippert through-frame style slide.
I had a similar problem as you described due to the poor installation of the styrofoam risers...., I had the slide roof repaired under warranty (removed EPDM & installed new riser)..
Also, don't rule out a possible slide adjustment issue as a possible root cause.
2016 GM 2500HD 6.0L/4.10
2018 Jay Flight 24RBS
2002 GM 2500HD 6.0L/4:10 (retired)
2005 Jayco Eagle 278FBS (retired)
1999 Jayco Eagle 246FB (retired)
Reese HP Dual Cam (Strait-Line)