Water coming up from the bed not from top

[D2500]

I have a 100% water seal on my truck bed cover. And have 2 bed rails on the deck show water leaking. After investigation there has to be a factory seal on the side rails that fills up with water and the overflow is on the exact sides of the bed.
Anyone else have this issue

 

[Sharkadile]

based on the location of those water trails ... my first assumption would be leaking from the 3 plastic cutouts on the bulkhead wall. any water that passes between cab and the bed could be seeping by those plugs.

 

[securityguy]

I agree with @Sharkadile as it does not appear to be coming rom the side rails. Maybe the rear window area gasket where the cover meets the front sill. No cover gives 100% water tight seal.