Hello
The first guess would be that there might be a custom event plugin which is change the state of all these jobs. Are you running any custom even plugin? Check in Deadline Monitor> Tools> Configure Events> check here.
If there are not any then this needs to be tested, it may be a bug. I will test and report back. If I understand correctly when the jobs are suspended and then pended then they retain their original dependency status which was done at the time of submission. Is that right?
If it is, the workaround could be to submit job as suspended and then pend them using the event plugin. Or do both suspension and resumption through an event plugin.