A run-time error is a bug in the source code. You should send a bug report to HEC. Until you hear back from them, you can go through all of your input data and make sure it is all correct and logical. If input data is all good, you may want to try a different version of HEC-RAS and see if that helps.
Definitely check your input data. The Ras Sediment functions do very little data validation. I’ve seen the “Object variable or With block variable not set” pop up as a result of trying to pass null data. Sometimes you cannot see this in the viewer so you may want to check your .s## input file which is ascii xml format.