I have exactly the same problem since 2 days and I spend almost the whole last night with tests (even disassembling my PS3 to check if something is broken with the USB connector on the mainboard)
First the facts about my system:
60GB PHAT (Cardreader + 4 USB Ports)
Model: CECHC04 (German PAL)
To put the PS3 into Service Mode i used an AT90USB162 with a PSGrade Hex (Teensy 1.0) from archive: psgrade-all-boards-fixed.zip
The downgrade worked pretty much fine as in Service Mode it shows now 3.41 (it was 3.55 GeoHot before) but actually it doesn't get out of Service Mode.
The reason for this is that the rightmost USB Port seems to be unpowered. I even checked with a Multimeter and there is no voltage at all on this port.
I even build a Y-USB Cable which is getting the +5 Volt from the 2nd USB port as i thought only the power for USB is missing on the right port but it still doesn't work as the port seems to be disabled on the Datalines.
Interestingly i can't get it to Service Mode again with the initial HEX that i used meaning: Usually you put the Teensyboard in one of the ports and start the console with Power -> Eject like in JB mode. Normally it should switch on and after a few seconds go automatically off. Instead it simply boots to Service Mode
I put now another PSgrade HEX (PS3key AT90USB162) on my 2nd Teensyboard and actually this one switches the console off automatically after a few seconds but still no success in getting the rightmost USB-Port to get powered and therefore it simply can't load the 202kb Lv2diag.self
When I put my HEX for 3.55 SPOOF HERMES or the equivalent (PL3) on the Teensyboard I even can Jailbreak in Service Mode. Meaning I could install a FTP Homebrew or Comgenies Awesome Filemanager.
Do you guys know if there is something like an Autostart Folder withing the dev_hdd0 in which we could probably copy the Lv2diag.self so it will load it automatically when we switch the PS3 on?
I know just a crazy idea but I'm really running out of Ideas. BTW. Sorry for my bad english I'm German. Hope to hear from you guys soon.
Kind regards, CableLeecher.