"I picture a box that contains a particle that travels back and forth at the speed of light."
Very good!
"[...] We place this box on the surface of a large planet. The particles run upwards and down, perpendicular to the surface."
As far as the relations between constituents of a box being held rigidly wrt. a mass can be approximated by relations between constituents of a box being uniformly (hyperbolically) and rigidly accelerated in a flat region, which can be calculated explicitly, the signal front roundtrip durations (ping durations) "top-to-bottom-to-top" and "bottom-to-top-to-bottom" are found as
$$\tau_{\text{TBT}} = \tau_{\text{BTB}} \, \text{Exp}\left[ \, \frac{a_B \, \tau_{\text{BTB}}}{2\, c^2} \, \right] = \tau_{\text{BTB}} \, \text{Exp}\left[ \, \frac{a_T \, \tau_{\text{TBT}}}{2\, c^2} \, \right],$$
where $a_B$ is the acceleration magnitude of the bottom, and $a_T$ is the acceleration magnitude of the top constituents of the box.
"One round trip is a unit of time."
The ping durations are separately constant (that's what we mean by constituents remaining rigid wrt. each other), and therefore separately useful "units". But these "units" are not necessary equal; especially, in consequence of the above equation:
$$\tau_{\text{TBT}} \gt \tau_{\text{BTB}}.$$
"it is predicted that the rate of time in a gravitational field will decrease"
At best, apparently that's a very cryptic and very much depreciated attempt to express, that between top and bottom constituents which are held rigid wrt. each other the (constant) ping durations "top-to-bottom-to-top" are larger than the (constant) ping durations "bottom-to-top-to-bottom",
$$\tau_{\text{TBT}} \gt \tau_{\text{BTB}}.$$
"Has the box been elongated?"
As far as "length" is understood in the sense of chronometric distance between two ends which are and remain at rest wrt. each other in a flat region, as
$$c/2 \, \text{Ping duration between the two ends},$$
any pair of bottom and top constituents of the box cannot be attributed a particular (mutually equal, symmetric) distance value, but two unequal values of quasidistance.
Of course, instead of "length", the term "height" is used when referring to spatial extension between rigidly held constituents ("directly above each other"), along the direction of acceleration. Nevertheless, it is not trivial to attribute exactly one "height" value to such a pair.
"If the speed of light is constant"
By definition, the speed of light (signal front) is constant between any pair of constituents (signal source and receiver) to whom a particular distance value can be attributed. Since this doesn't apply to any pair of one top and one bottom constituent of the box, therefore there cannot be any particular "speed" value be attributed to whatever would be exchanged between top and bottom, or vice versa.