MacBook Pro Three beeps - RAM Test passed

Hey,
my MacBook Pro (Early 2011, 2.0 GHz, Mountain Lion 10.8.4, 8 GB RAM, 256 GB SSD + 500 GB HDD) recently began to freeze or power off and then playing three beeps instead of turning on again.
The problems began some weeks ago, as the file system on my SSD (I've switched the Superdrive with my HDD and put in an additional SSD myself) broke and could not be repaired by Disk Utility. So I formatted the partition and reinstalled Mountain Lion. Since then my Mac crashed three times with (logged) Kernel Panics.
In the interim it's running quite stable, but it froze in the past two or three days several times while I was using it (for example playing a YouTube video or a MP4-File saved on my harddrive) and then began to beep three times. I know this should indicate some kind of RAM issue.
The first time the beeping occured, my Mac began to work again after I carried it over to a friend without opening it at all. Then I ran the Apple Hardware Test (short version) and it passed, later I also ran the extended version and it passed as well. The memtest utility also finds no error.
The latest crash was a bit harder. I took out the 8 GB RAM (I've upgraded from original 4 GB) and reinstalled the original "Apple" 4 GB RAM that came with my MacBook - still three beeps. So I took them out and just put in one bar of my RAM (so one of the two 4 GB bars) and it booted just fine. I wanted to rule out a defect of my logic board, so I tried the following combinations of installed RAM:
first bar in the first slot      - boots
first bar in the second slot - boots
second bar in the first slot - boots
second bar in the second slot - boots
both bars installed  - boots
Another thing that happened recently: I put my Mac to sleep with ~25% battery left, it was then laid to the ground. After I picked it up maybe an hour later it didn't power on when I opened the lid and also didn't when I hit the power button. So i plugged it in and it loaded the saved memory from the SSD - but the display just showed a resolution of about 800 by 600 pixels. It booted to the login screen, I entered my password and then it restarted automatically (still with low resolution), booted with the apple logo, crashed again and booted directly to the recovery partition. I tried to choose the Mountain Lion partition to reboot from, but it wasn't listed (instead I just saw the Bootcamp partition on my HDD). I powered it off and on again, hitting the option key to see all my drives and voilà, all partitions were listed (ML, Bootcamp and Recovery) and the Mac booted successfully to the login screen, where it restored the correct resolution of 1680*1050.
I don't know what to do, since the RAM bars don't seem to be the problem (since they are passing the test, running fine in between and the original RAM also produced three beeps). It seems to be the logic board, but the crashes occur quite random and it's not as if one RAM slot was totally broken. As the problems started with a broken file system, could it also be the SSD (although the SMART-Status is still verified)?
I hope anyone can help me or at least give a useful advice.

I would like to give you few pointers that may give you some relief. First, your problems sound almost identical to mine. The timeline is almost identical as well. After following the advice from the Apple Support Tech, we finally arrived at the conclusion that it is a hardware problem with my late model MacBook Pro 2011. The Apple support tech asked me to take it in for service. Since I had over 10 hours before my appointment, I did some additional diagnostic and made some discoveries.  I will outline my steps below to show how I arrived at my conclusion.
Problem:  MacBook beeps 3 times and freezes, BSD dump on screen or frezzes and restarts with appropriate fail message.
Apple: Use original 8gig Apple ram, Boot into Diagnostic utility and restore 10.7 OS, restore backup from time machine.
Solution: Everything worked fine, no more crashes. Restored TimeMachine backup using Diagnostic utility.
Problem: Booted fine, after 15 minutes, went into recursive white screen of death, as I like to call it.
Apple: Sounds like a hardware issue, scheduled Apple Store visit.
Solution: Removed SSHD (seagate hybrid) and reinstalled MacBook HD. Updated to current OS, 10.8.4, did not restore any of TimeMachine backups. Running CPU, ram, HD stress tests for several hours without a crash or freeze.
Called Apple support and cancelled my Apple store visit and determined to allow more stress tests to run over night and also testing the SSHD outside using SeaTools for any problems with the drive. So far none after 4 hours of testing.
Conclusion: During the past several months as Apple has been updating the OS, I belive the applications and utilities that are running on my machine may be causing the crashes of the MacBook pro. My suggestion is to Make a backup if you do not do this daily. Restore OS from Diagnostic utility and update OS. Do not install any third party utilities that alter OS or enhance the OS operations. Reinstall your programs from scratch. Use migrations utility to restore only the data associated with your programs. I believe that you will avoid restoring any programs that might cause your crashes. I also suggest you run a day or two without restoring anything just to confirm your MacBook is operating well. I will keep you posted after I finish in two days as to the outcome. But I am certain it is not a hardware issue at this point.

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