David,
We were given a new version of softmon.exe, it is the one that is supposed to come out with SP1. We were told that during the agent install, softmon.exe was messing up some app permissions and that the new one fixes that. We replaced our existing 9.6 softmon.exe with the new one. For new deployments it resolved the issue. Windows Store Apps worked fine as well as Windows Desktop Apps. We were pretty excited. We decided to abandon the 20 or so machines we deployed 9.6 to and to reimage them. This was up until we noticed the reimaged systems ran sluggish. It turns out that the new Softmon.exe introduced some new bugs and caused our CPU's to spike. We use the LANDesk Antivirus product (Kaspersky) and it was using 20-30% CPU as well as softmon.exe was using it's own 20-30%. Softmon.exe started writing a softmon.log file and it wrote just under 10,000 lines in the log per second. It would max out, rename itself and start another log. Eventually it is smart enough to only keep 3 versions of itself and it didn't fill the drive up. Anyhow, we disabled Software Monitoring in the agent and scheduled an agent update. This brought the CPU utilization back to normal. Now, I gave all of this to LANDesk and their engineers are looking at it. I am very hopeful that they will be using my data to rework softmon.exe some more before releasing 9.6 SP1. I hope you got false information because this is a big deal for us and is not acceptable. Also, the new softmon.exe caused our Windows 7 machines to behave the same way in regards to the CPU utilization. So, now we can use Store apps in Windows 8 and 8.1, but we cannot use software monitoring on anything because if we do it affects everything!
I would hold off on continuing any 9.6 deployments until these issues are resolved. Who knows what else softmon.exe does. The original 9.6 version has bugs that effect Windows 8, we know that, but what about the stuff we don't know or haven't discovered with Windows 7, Server, etc. I do not trust it and I don't think you should as of yet. I will post more updates here as I get more information from engineering. I have several active tickets open and have been promised that they are being worked on with a high priority.