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This question has been answered by mr.odo. See the first response.
Are you maybe clicking on "Save Property Set" without selecting the property set in the drop-down on the Properties tab of the Create/Edit snippet panel? That might save the default properties to the property set, which would empty it.
Clicking on "Revert All to Default" when editing the property set would also explain it.
It sounds like the default properties are being saved as your property set. Since there are no differences, the property set's properties are empty.
Are you using modx 2.4? This is the known bug of a new version.
Here is the bug report and bugfix https://github.com/modxcms/revolution/issues/12580
MODX Revolution 2.4.1—Updates & Fixes
The latest release of MODX Revolution is a patch upgrade to 2.4.1. If you missed the 2.4.0 announcement, get the low-down here. Lots of goodies.
opengeek added this to the v2.4.2-pl milestone 4 days ago[ed. note: mr.odo last edited this post 8 years, 6 months ago.]
https://github.com/modxcms/revolution/milestones/v2.4.2-pl
MODX Revolution 2.4.2-pl (October 6, 2015)
====================================
- Fix emptying property sets on element save [#12580]
- Different tree styles for unpublished + hidemenu [#12699]
- Add patch for ExtJS Drag & Drop issue [#12617]
...