I have three controllers that I've bought over the last few years, all of them flash until their done charging. When they are full they stop charging automatically and the lights go out, so you know it's done. Not only does automatic charge cutoff save the battery, it allows you to use the controller plugged in for as long as you like without harm.
If you're gonna charge a PS3 controller with a charger that is not using the USB power standard, then you might make a problem for your controller.
PSN: CrashLanding (please ID requests as AVS)