In a natural man, i.e. not on HRT, endurance exercise has been shown in some cases to decrease testosterone as opposed to weights and resistance training which has been shown to increase it. I'm not saying you shouldn't do endurance exercise, by the way, but am just pointing out it can lead to decreases.
Of course, overtraining can affect hormones as well:http://www.peaktesteosterone.com/overtrain
The issue is probably that you are on a two week cycle. The last 3 or 4 days of a two week cycle will leave you pretty much hypogonadal and this is why most savvy docs do a weekly cycle from what I've seen. This also creates less estrogen spikes as well.
Again, weekly injections leads to smoother testosterone levels on average and less estrogen spikes and does not leave you hypogonadal the last three or four days. Big advantages, don't you think?
I hope he/she also pulled your estradiol. If so, can you send that?
Also, did you get your pull near the end of your cycle? If so, that's probably why your readings are so low.