Permanent negative water breathing after loading resource pack.

I attempted to create and load a resource pack for my world. All I had set for the pack was a single texture change for a single block (mud bricks).  The texture loaded fine but it also created a permanent "effect"; water breathing that never goes lower than 10 seconds untll you go in the water at which time it starts counting down. No use or /effect clear by chat or command block has effected the glitch effect. Using a totem of undying did not work. Having a command block to permanently set water breathing to 10000 did not fix the issue. When I loaded my world I had another effect permanently active via a command block; /effect @p jump_boost 24000 4 true.  I attempted to set both jump boost and water breathing to 10000 in the command blocks and this works unless I go in water at which time the tickers on both effects begin immediately counting down as if the command blocks are no longer working.  What could have caused this glitch and how can I fix it?