Same thing happened to me as well this season. Got a collection of tendon injuries (still aren't sure exactly what, but could be posterior tibial/achilles issues) that I have been dealing with for the past 5 weeks. After it started, I biked for about 1.5 weeks, then raced a solid 1 minute slower than I did on a 3 mile course that I had PRed on a week before my injury. Of course, it was still hurting, so I biked for another 1.5 weeks and was 1.5 minutes slower than my best time on a flat course. Started tentatively running on it again for a week, raced the same course as prior, and was only a few seconds better. Continued running the next (this past) week, and started to see a bit more improvement (ran a 5k on a hilly course in the same time as my poor 3 mile performance on a flat course), but still feel like I lost so much. Now I'm taking 3 weeks off to let the tendons fully heal and am trying not to think about how much fitness I might lose during this period. I noticed the same thing happening with getting more tired after about 2 miles in my races. I know I was pretty aerobically weak even before my injury, so maybe it could be connected to not having built up enough of an aerobic base? I'm interested as well in what other posters think.