I'm glad that it wasn't hard drive-related for you. For me, however, it was. I tried EVERYTHING to resolve it, as outlined in this thread, and nothing worked except replacing the hard drive. Oh well. It's entirely possible that this issue may be caused by any one of a number of factors, all leading to the same result.
There is still a fairly large part of me that thinks that this was update-related in some way, as I take extremely good care of my system and had no problems until the recent update. I hope, for the sake of all that are experiencing this problem with no solution yet, that Sony can provide a patch. Unfortuantely, I have heard that the good folks at Sony do not regularly check these boards, so I'm not sure if a fix is on the horizon or not...
If he is experiencing the issue the same way I did, none of the "usual" fixes will work. I tried everything you are suggesting, to no avail. Thanks for the suggestions, though!
Just to add to the evidence, my original 6axis controllers no longer work unless they are plugged in. I attributed it to dead batteries (as they are both about 5 years old and battery longevity of them has been decreasing more and more) but it could also be related to your issue. Either way, my Dualshock 3 is working fine still.
Ever since the update to 4.00 I have been getting this issue.
If I press the PS button on the controller to turn the console on, the console will turn on, but the controller will just stay flashing.
If I then turn the console off, the controller also shuts off. (So clearly the power on/off signals to/from the controller work)
But the ONLY way I've been able to get it to connect is to turn the console on with the consoles power button, wait for it to completely boot, THEN turn the controller on with it's PS button.
this has only occurred since 4.00 and is happening with ALL 3 of my genuine Sony SIXAXIS DualShock3 controllers.
This ALSO happens with my Sony BD Remote. if I turn the console on with it, I cant use it. if I turn the console on manually, then press the PS button on the BD Remote, after the console has finished booting, it works.
My console is the "CECH J" model.
Nothing wrong with my controllers batteries. they still work for about 10 hours of straight game play before they need charging. (Which is good, only USB charge cable I can find is 3 inches long, so I HAVE to use wireless.)
I think it may have something to do with the mandatory Epilepsy warning that makes the boot time longer, and thus maybe the controllers are reaching "timeout" without the console responding because of it. - That's just my theory.
I to have this issue. Ive also had problems with demo's stuttering, and games and netflix taking longer than normal to load. However maybe one in every five start ups I have no problems. No new HDD in this system, still the same one that came with it. Ive tried formating quick, full, and via my PC. Restore settings, reinstalling firmware, etc, etc. Strangely enough it did not start happening until a little after the 4.00 update. Although I know plenty of folks on here do not believe firmware updates can cause any problems of any sort. I may just wait until 4.01 or whatver it may be called, and see if it fixes it, otherwise I plan on just buying a new HDD, because I cannot think of any other way to fix these problems. Just an FYI, I have a PS3 Slim 120gb, bought it from a buddy january 2011, its been formatted so hardly anything is on it, ive vaccumed it out, pretty much anything and everything beyond buying a new HDD, which I am loathe to do since money is somewhat tight right now.
I know this will sound dumb, but have you tried going to Settings>Accessories>Calibrate Controller? I had the same issue on Tuesday (Feb 14, 2012), I'd gone out and bought Twisted Metal Limieted Edition, and after installing the bonus Twisted Metal:Black that came with as DLC, went to try TM:Black quickly. in PS2 mode (more or less the same as PSone classics, but PS2), the controllers worked fine. When I went to quit game, I noticed EXACTLY what you were talking about in your OP, they'd just auto-off instantly after rapid flashing, and only way they'd connect to the PS3 was to USB sync, which when I unplugged, more flashing & auto-off. I'd even tried Move Motion & Nav controllers, even my BD Remote, nothin would work.
I had to power off 100% (not even a red light when off,NO POWER to it at all, plug it back it, power up again, and still did the same thing, nothin would work. so 3rd time, I powered off comletely (no red light again), plugged back in, made sure DualShocks were hooked up by USB, and when I started this time, I went into Calibrate Controller, and after that, everything worked again.
dunno if it'll help you or not, or if you've tried it already, but seemed to have fixed my issue that way.
when you turn on your ps3 just plug the controller in untill it syncs and if you use it on both of your ps3's than thats why its being wierd becuse i went to my friends house and one of his ps3s kept on freezing so we went upstairs and used his other ps3 and it wouldnt sync so we used the cord and it synced hope this helps