The choice of:
- positive axis is arbitrary (whether up/down or left/right as positive does not make a difference in the solution).
- direction of unknown vector quantities is also arbitrary. i.e. you draw the unknown quantity as positive or negative and if the equations are properly constructed then the sign will indicate the true direction.
The most common problem in dynamics problems is what happens with derived quantities e.g. moment of an unknown force. More specifically, if it required to determine the moment of a $m\ddot{x}$ term (which describes an "active" force), then depending on the position of the $m\ddot{x}$ relative to the point that the moments are calculated the resulting moment can have a positive or negative sign.
An additional example --which commonly produces confusion -- is the term $J \cdot \ddot{\theta}$. Although the positive direction for $\theta$ is defined as ClockWise(CW), the moment is positive for CounterClockWise (CCW). So in this case, I suspect what is happening is that whoever drew the diagram drew the term $J \cdot \ddot{\theta}$ as positive with respect to the moment positive.
Apart from that I am not certain that in this problem you can ignore gravity. Which means that the force on the rope will not be equal to $m\cdot \ddot{x}$ (it can actually be derived by $m\cdot g -T = m\cdot \ddot{x}$).
Also, I agree with you that $\ddot{x}$ should be pointing downwards, if $\theta $is rotating counterclockwise (unless $\dot{\theta}$ is too large).
However, in general it will be very difficult to decypher what was the exact methodology that the person used to derive the equation (or his/her intent),without a more detailed explanation of the solution. .