So we originally had a JDS running on a RHEL server handling our package deployments that we had to wipe down after we upgraded to 9.81. In the mean time I pulled a Mac Mini and setup a SMB distro point that has been working while I rebuilt the JDS. Now that is is back up and running we are experiencing some odd things when we try to replicate packages from the Mini to the JDS. In Casper Admin it will run the replication process and say it finishes successfully, but only a couple packages move across. I've given the process a couple hours to finish the sync between the database and the JDS, but nothing else comes through.
I'm also having some strange issues with jamfds inventory where it tells me requires root, but when I add sudo to the beginning it tells me command not found.
I have experienced similar issues myself, however I have not had a lot of time to dig into them. I'm also in the process of getting rid of our AFP distribution points (running on minis)... and replacing them with JDS instances on RHEL. I figured the issue may be something due to checksums... or some sort of incompatibility between OS X and RHEL. Again, I haven't had a lot of time to dig into the issue on my end. I'll try to post my experience (I may end up opening a ticket).
I am running the JDS on CentOS, I do "su -" to switch to the root user then run jamfds and it works (remember to leave out the sudo, since you are already the root user). For the syncing issue, check the log file (/usr/local/jds/logs/jamf.log), that might have the error in it.
@Jerod I'm also on CentOS and I just tried that and it still throws the command not found error. The logs were interesting to look through as they start the download, finish and error out saying the package "failed to download correctly - deleteing local copy"
I may just come in after hours and rip out the SMB share and reupload the packages to the JDS through the JSS interface and see how that goes.