When you say a couple of years ago that you got your brake set up, have they ever been bled and maintained at all? Mineral oil systems like the Shimano hydraulic brakes need a little more maintaining and don't take containment as well as DOT fluid brakes.
If this is your yearly commuter bike, I would recommend at least a bled annually, but preferably every 6 months. What are the condition of your rotors and your pads?
What you are describing sounds like water in the system, moisture can get into hoses and hydraulic brake systems.
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