Take a look at your relationships and see if the "delete" option has been enabled. The most common cause of seeing multiple records deleted when you delete just one record is that you have this option specified in one or more relationships. This can result in a "cascading delete" that can indeed delete most of the records in your database or just a few like you describe here.
To check this, open manage | database | Relationships and double click each relationship line. Look for cases where the "Delete related records in this table when a record is deleted in the other table" check box has been selected.
OMG...this is a lifesaver! I was having very horrible experiences with deleting multiple similar records. Thank you! I hope this solves all of the issues!