Electronic – Amplify 29 kHz signal

That looks like a sine wave with the y-axis wrapped around. Here's my attempt at recreating it:

This is a plot of the function \$1.25 \cdot \sin(t) - \operatorname{round}(1.25 \cdot \sin(t))\$, where \$\operatorname{round}(x)\$ rounds \$x\$ to the nearest integer.

Perhaps the highest bit of your signal is getting cut off? That would seem likely to produce such a waveform.

What you have is a succession of low pass RC filters operating on a square wave followed by an active filter. As each filter takes effect, the waveform becomes rounder since its high frequency components are being reduced in magnitude. Calculating the value of the sine wave voltage, which includes the effects of all of the filters, is a difficult paper calculation because the filters interact. Since R4, R5, and R6 are the same value, each RC stage affects the one preceding it. Your best bet is to use a circuit analysis program.