The combat action run says
You can run as a full-round action. (If you do, you do not also get a 5-foot step.) When you run, you can move up to four times your speed in a straight line (or three times your speed if you’re in heavy armor). You lose any Dexterity bonus to AC unless you have the Run feat. (Player's Handbook 144)
(Links mine.) Unlike the special attack charge that specifically says that a creature that charges suffers "a −2 penalty to [its] AC until the start of [its] next turn" (PH 155), a creature that takes the action run seems to be lose its Dexterity bonus to Armor Class only while running on its own turn, regaining its Dexterity bonus to Armor Class upon its turn ending—that is, when it stops running.
However, my players were shocked during a recent session when the advanced mama phargion (Miniatures Handbook 66) took the action run on her turn and I said that on their turns—after mama phargion had taken her turn but before mama phargion had taken her next turn—that mama phargion was not losing her Dexterity bonus to Armor Class against the PCs' attacks.
My players said that their PCs should be making their attacks against a mama phargion that had lost her Dexterity bonus to AC because she ran on her turn and she hasn't yet started her next turn. I said for that to be the case, either the action run must have an exception like the special attack charge or the action run must take not a full-round action to perform but, instead, a 1-round action to perform (like casting a spell with a 1-round casting time). (This latter option would also mean the runner wouldn't reach its destination until right before its next turn—as if combat weren't complicated enough already!)
Did I rule correctly? Does a creature that takes the action run only lose its Dexterity bonus to Armor Class during its own turn, or does a creature that takes the action run lose its Dexterity bonus to Armor Class until the start of its next turn? Or is there even more to this than I realize?