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I found the same problem with System Explorer v5.9.4
I am having related problems with System Explorer 5.9.2 and 5.9.4 with Win8.1U1 Pro x64.  Process Explorer shows about 50 processes, while SE shows about 5.  I saw this problem with SE even before I installed Sandboxie.
I found the same problem with System Explorer v5.9.2
I found the same problem with System Explorer v5.9.0.
I found the same problem with System Explorer v5.8.0.
Issue still exists in SE v5.5.0.
I followed your advice, and it worked!  Thanks.  I will keep SE v5.0.1 installed now.

I saw that you mentioned the new history behavior in your news post, but I was having trouble understanding what changed.  For example, processes are still monitored in the History tab even when the Processes tab is closed.  This is a good thing, but the behavior is different than with net connections monitoring.  Maybe it would be helpful to add a tip to the History tab reminding users how to enable items that are currently not monitored.

When I enable the Opened Files tab, files are not monitored in the History tab.  Was the files monitoring feature lost in SE v5.X?

When I have the History tab enabled, I always want to monitor events, but do I need to have another tab open to enable monitoring them?  Or is net connections the only optional item monitored in the History tab?