I have a world where I have been working on kitpvp, and each kit has it's own effects. Recently, I checked the effect one of the kits gave me and sure enough, it seemed unbalanced. I checked my command block, thinking I had made an error but to no avail. I tested it with everythimg else and I still had the +1 problem (Everytime I gain an effect via command, the game adds one to at least to the displayed value). I tested it and it works with typed commands too, not just command blocks.
Tl;dr: Effect command adds one value to effect value when commands are used to give said effect.