What could have happened?

You or someone else DROPed or RENAMEd the table? You USEd the wrong database?

Have you encountered this sort of things before?

No and to be realistic it is unlikely that you have uncovered a bug in MySQL. The spontanteous loss of tables is the kind of thing people notice. You can see if what is really there by looking at the raw data dir. A database is a directory. A table is 3 files within that directory. For example:

[root@devel3 mysql]# locate mysql/test
/var/lib/mysql/test
/var/lib/mysql/test/testac.frm
/var/lib/mysql/test/testac.MYI
/var/lib/mysql/test/testac.MYD
/var/lib/mysql/test/base.frm
/var/lib/mysql/test/base.MYI
/var/lib/mysql/test/base.MYD
[download]

My mysql data dir is /var/lib/mysql. The test database has two tables called 'testac' and 'base'. If by chance you can see the .frm, MYI and .MYD tables that correspond to your table check their perms. You could just do 'locate -u; locate missing_table.MYD