Apologies if it's bad form to necro a post like this, but I might have found a workaround for a similar issue in FT 3.5.1. The workaround is only useful if you haven't done much manual offset editing. I'm commenting in case users like me have this problem in the future.

My symptoms were a bit different, but I think they had the same cause: somehow, I ended up with a smallish area with preposterous depth (way over -40k, iirc) near 180 longitude. I think something in the basin-filling, land-expanding, or incise flow tool went ballistic. When I tried to find rivers, it wouldn't show anything unless I slid the slider way over to the long end, and then the rivers showed as big wads over random spots in the ocean. (I think the spots even stayed the same in screen space if I rotate the world and try again, but I could be remembering wrong.)

Workaround: I worked around it using clues from jslayton's post above. Tools > Global Set > Land Offset Edit > 0, which unfortunately erases manual offset edits and actions like fill basins and expand land. This switched the bazillion-deep spot near 180 longitude to a quite high spot, and rivers started working again. I edited the spot with pre-scale offset to get it down to a reasonable depth.