Ah, the tBIN map format does not support storing a per-frame duration. The only way to make a frame appear longer when you need to use tBIN is to repeat it in the list.
Now that I write this, it occurs to me that maybe Tiled could make a best-effort to match the animation you’ve specified by automatically repeating frames. Then it would need to specify the shortest frame time as the frame duration and repeat longer frames as needed. Of course, it could lead to very long animations in some cases.
In any case, a warning is in order just like with saving of tile rotations, which also isn’t supported by the tBIN format. The upcoming Tiled 1.3 will feature a proper place where such errors / warnings can be reported.
Are you modding Stardew Valley or using tBIN for some other reason?