System File Permission settings have no effect on what open/hosted files appear when you select Open Remote...
Here's one possible issue you can check: FMP installer does not install server.pem file
This is one of many acknowledged bugs that can be found in the Known Bug List here in the Report an Issue section of the forum.
It can also be downloaded as a database file from: http://www.4shared.com/file/8orL8apk/FMP_Bugs.html
Did you get this issue resloved?
No. But it is related to Windows 7 on the specific computer. I can load FMS onto another workstation running Win 7 Pro and all opened files are available and FMS behaved as expected. I believe it is a Windows Firewall/security setting on the original computer that no one could resolve.