Half-wave rectifier and RMS value
Let's take a look at the signal waveforms:



You are right there is a diode voltage drop, let's assume for all intents and purposes the diode forward voltage drop is \$0.635V\$.

To compute the RMS voltage:

$$ V_{rms} = \sqrt{\frac{1}{p} \int_0^p V(t)^2 dt} $$

where \$p\$ is the period (in this case 1ms).

What is the output voltage?

Let's assume for a second that when \$V_{IN} &lt; V_{DIODE}\$, \$V_{OUT} = 0\$. This isn't quite true, but should get us close to the correct answer.

So our output voltage for one period is:

\begin{equation}
V_{OUT} = \left\{
\begin{array}{lr}
0 &amp; : 20\mu s &lt; t\\
5 \sin(1000 \cdot 2 \pi t) - 0.635 &amp; : \text{otherwise}\\
0 &amp; : t &gt; 480\mu s
\end{array}\right.
\end{equation}

plugging into the \$V_{rms}\$ calculation,

\begin{equation}
V_{rms} = \sqrt{\frac{1}{1 ms}\int_{20\mu s}^{480 \mu s}(5 \sin(1000 \cdot 2 \pi t) - 0.635)^2 dt} \approx 2.1V
\end{equation}

The minor difference in calculated values here and your measured values are due to the assumptions I made about diode behavior (constant diode voltage drop, \$V_{OUT}\$ behavior when diode isn't saturated), as well as component behavior not being ideal, nor having exactly the same characteristics as those I chose for the calculations.

Ok, what was the average voltage across the same time period?

\begin{equation}
V_{avg} = \frac{1}{p} \int_0^p V(t) dt\\
V_{avg} = \frac{1}{1 ms}\int_{20\mu s}^{480 \mu s}(5 \sin(1000 \cdot 2 \pi t) - 0.635) dt \approx 1.287V
\end{equation}