I observed the problem when I implemented support for PROPERTIES in eix:
Although there is some azColName "PROPERTIES" stored in the sqlite database,
the corresponding entry is always empty (after emerge --metadata with
portdbapi.auxdbmodule = cache.sqlite.database
eclass_cache.dbmodule = cache.sqlite.database
in /etc/portage/modules) even for those packages for which it is nonempty in
the /usr/portage/metadata/cache database.
Other metadata like azColName "RESTRICT" does not have such a problem.
For the case that it is important: pysqlite-2.3.5 and sqlite-3.5.9 are used.
This is fixed in svn r11560.
This is fixed in 2.2_rc12.
If you run emerge --metadata then it should update the PROPERTIES values.