Ok I had this same problem.
I registered to post what happened to me and how I got it resolved.
I bought a 40GB ps3 from Wal-mart on May 8th. I had saved for a while and the price drop helped me purchase it. I wanted to play GTA4 and COD4 (both great games)
Well every time I powered the system off for more than 2 hours (standby mode) when I went to turn it on w/ the sixaxis ps button wirelessly, the system would power up, the sixaxis 4 flashing lights would blink...and the screen would eventually tell me to plug the controller in the USB and hit the ps button. Which I did. Sometimes i had to do it twice because the system wouldn't boot up.
Then it would pair, and the ps3 would start up, and I could unplug the usb and it wokred fine. This even happened if I turned the system on with the usb already attached. I called sony, went though a) resetting the contoller with button on the back. b) restore default settings (which makes you re-pair sixaxis) and c) hard reset (turning the entire power off and holding the power button while switching on the main power and getting the two beeps.
None of this worked however, after 2 hours with the system in standby same thing happened. So I googled around, found this page...
I backed up my game saves, formatted the entire system. Same thing. I was fed up because the sony rep told me to narrow it down to take my sixaxis to another ps3 and see if it loses connection to another ps3. Bullcrap I shouldn't have to go to another ps3, that's a cop out.
So after debating to either call sony and demand a replacement or go back to Wal-mart (gotta love the walmart return policy. I decided I would go to wal-mart. Told them it was defective. They bring me a new ps3 from the back, so they exchange, and guess what...wal-mart has a promotional deal this week (June 1-7) ... after 45 minutes of confusion at the customer service counter, I walked out with a brand new ps3 and a $100 gift card for wal-mart because of a ps3 40gb promotional deal.
Hooked my new ps3 up, charged the sixaxis... put the system in standby overnight. Got up this morning and fired it up, and it synced right up. No problems at all.
Just posting this because it was driving me crazy..Sony would not admit anything and wanted to send me a box, ship my ps3 to them, and wait for a new one to come in the mail. Meanwhile I went to my retailer (something sony does NOT want you to do) and ended up with $100 and getting a non-defective unit.
I really think it's either the sixaxis controller that was defective...or the bluetooth antenna in the ps3... It looks like by researching online that it has only been the 40gb model.
Hope this helps someone.