This is good info to have. I have been running into a similar problem and believed it was some form issue causing the imbalanced fatigue. While my form is definitely a work in progress, I am glad to hear that there might just be some muscle adaptation happening alongside.
I think it's a combination of specific paddling strength and form/technique. They both get better with time on the water.
I remember one summer when I was in the best paddling shape I'd ever been in. I won the Jensen Handicap race in Minnesota that summer (lucky draw for a great partner). The next year I started building my own house and had only been on the water a couple times for leisurely paddles. The race has a traveling trophy so when I came back to return the trophy the next summer I decided to race since I was there anyway and what a difference it was!
I felt like I had nothing to give. I felt strong at the start but soon I felt very fatigued and I couldn't sprint to save my life. I could maintain a steady power but I just did not have a higher gear to kick into. I didn't feel out of breath, just like I had no power. I doubt my form or technique had degraded that much but those paddling muscles sure had.
Alan