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The beads of sealant are common...., they seal the metal trim edges where it makes contact with the roofing material. In most applications a heavy application of self-leveling caulk would cover the metal trim rail and flow over the edges onto the roofing material.
Also not unusual for standing water on some of the older models because some models like the Jay Feather had very little roof pitch incorporated. This was most notable around the front/rear cap joints, and the A/C.
Removing the interior wall/ceiling panels would expose insulation and framing. In your case you may also find some moisture damage and/or mold.
Bob
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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)