Certain spells and abilities give players the option to add the Flaming property et al to weapons in the middle of combat. The Magus arcane pool class ability, for example.
By this RAW, it would seem that in addition to whatever action it is to add the property, a character then has to command the weapon to activate as a standard action. Which, if true, is a huge downside to such powers.
No...if you add/activate the properties from a class ability, then the specific rules on that class abilities action requirement would override the general rules of activation of the property by my understanding.