So I do have a couple more comments. First, assuming that your probe protrudes 1.25" into the pipe (1" to get the hole into the center and another 0.25" since the hole can't be at the end of the tube), then the probe is still going to be blocking 10% of the area of the pipe, so it will definitely still cause the flow to accelerate just by being in there.
Second, let's assume for a second that your probe is just hanging out in a wide open area with no pipe to worry about. If the air is moving toward it at some velocity ##U##, then the velocity parallel to the surface of your tube at the surface is going to theoretically be
[tex]v_{\theta} = -2U\sin \theta,[/tex]
where ##\theta## is the angle around your probe (starting at zero on the right horizontal and measured counterclockwise). This is using potential flow theory, so it isn't perfect, but it's a decent estimate for the time being. In other words, over the top of your probe, the magnitude of the flow velocity is going to be roughly twice that of your incoming free stream. The flow should still stagnate at the front end, but the problem is that your hole that you are using as a pressure tap is not infinitely small, so it is measuring more than just the tiny bit of flow at the stagnation point.
If your tube OD is 0.25", let's assume the hole you drilled is 0.125". That means that your hole is going to take up 60° of the circle. Using that, we can average the velocity you are actually measuring. First, look at the "stagnation" condition. The relevant problem here is integrating the velocity ##\pm \pi/6## about the measurement point to find the average (this is just in one dimension, I haven't even considered the second dimension of the hole). So, getting the average velocity of the flow over your hole is just solving
[tex]v_{avg} = \dfrac{2U}{\frac{7\pi}{6} - \frac{5\pi}{6}}\int\limits_{5\pi/6}^{7\pi/6}|sin\theta|\;d\theta \approx 0.512 U,[/tex]
where I've taken the absolute value since we are looking to average the magnitude here. You are therefore measuring nearly half of your free stream velocity there, not stagnation. Doing the same thing for your "static port" configuration is solving
[tex]v_{avg} = \dfrac{2U}{\frac{2\pi}{3} - \frac{\pi}{3}}\int\limits_{2\pi/3}^{\pi/3}|sin\theta|\;d\theta \approx 1.910 U,[/tex]
so you are measuring nearly twice your free stream velocity there. In other words, you shouldn't expect these to measure what you are hoping they will measure. I don't particularly feel like working out the double integral to get a more accurate estimate based on two dimensions, but it will tend to make your static port worse and your stagnation port a little bit better. Either way, it's not a good design.