64 bit kernel cabable iMac won't boot in 64 bit kernel when prompted in Mountain Lion.

I'd doubt the 3rd party App.

There is no 32 bit kernel in Mountain Lion.

You can check in Activity Monitor.

So to check, fire up Activity Monitor. In the box along the top show "All Processes." Then control click on the column header (say, on "Process Name") and ensure the "Kind" checkbox is checked.

Once you've done that, look for "kernel_task" in the list (It has PID 0) and see that Kind says Intel (64 bit).

I know this is as old as heck thread but did you ever get to the bottom of this issue? I recently updated to the latest Yosemite 10.10.5 on a late-2011 13" MacBook Pro and ever since I'm having the exact same issue described above. I have always booted into 64bit but now it doesn't seem like it is an option anymore. The worst part is that it seems this issue is causing all sorts of kernel panics, software and browser crashes that I previously didn't have literally up to the moment I updated. Laptop is basically unusable at this point. Besides poor batter performance everything was working fine up until the update with no indications of problems on the way. Tested the RAM in diagnostics mode and it checked out okay. Did PRAM and SMC resets. Repaired all permissions and disks. Even went as far as to wipe HD and re-install OS X Yosemite from scratch. Still having same issues. It's as if something has permanently happened to the 64-bit kernel and now everything is crashing because it's gone MIA... My next step would be to roll back to an older OS and see if same issues persist...

Like Hunter I previously I also had the 64-bit verification in System Software Overview but now it's gone. I also used the same 3rd-party app to verify as never had a problem with it before. Upon loading it it previously would display all four fields as 64-bit. Now just the first three are 64-bit while the kernel is now stuck at 32-bit. Can't use the app, can't hold '6' + '4' on reboot and can't even modify the boot file to force it to boot into 64-bit.

Called Apple and when to Apple store but both option just resulted in them saying it is possible that the logic board coincidentally failed at the same time I updated the software so their default response was to book it in for a logic board replacement.

I can't help but think it isn't just "coincidental" as they say. Don't know if this is the old conspiracy theory of "Apple Planned Obsolescence" in action but considering the timing of how things when suddenly belly up.

Never use such utilities on a system that is already 64 bit. It tries to accomplish the changes by writing to the NVRAM. Most likely, it screwed things up. Mountain Lion and later will only boot to 64 bit systems, so there was nothing to check to begin with.

Restart and hold down the Command+Option+P+R keys to clear the NVRAM of any changes. Keep holding the keys through two startup chimes. It will be set back to its defaults.

Check System Information again. It should be displaying properly again.

I have tried the Command+Option+P+R to clear the NVRAM (I mistakenly identified it a PRAM) but nothing changes. Also I remember that the MacBook came with Mountain Lion yet was 32-Bit default so I still had to force it into 64-Bit using the utility shown above. Had to do it every time a new OS would come out. Never had any issue upon doing so...till now.

A late 2011 MacBook Pro would have come with Lion and been preset to startup in 32 bit mode. Sounds like you purchased it used and was sold with Mountain Lion installed.

I would strongly suggest ditching that utility. The much safer way to switch startup modes is by modifying a file on the drive. There are two different Terminal sets that work depending on how old your system is. Yours likely uses these:

To set your machine to boot into 64 bit mode enter this command and reboot:

sudo systemsetup -setkernelbootarchitecture x86_64

To set your machine to boot into 32 bit mode enter this command and reboot:

sudo systemsetup -setkernelbootarchitecture i386

The other set applies to older 32/64 bit models (like our 2008 Mac Pro):

sudo defaults write /Library/Preferences/SystemConfiguration/com.apple.Boot 'Kernel Flags' 'arch=x86_64'

To return to 32 bit mode, you would repeat the command but enter an empty string, which would just be the single quotes (where arch=x86_64 is) with nothing in between.

sudo defaults write /Library/Preferences/SystemConfiguration/com.apple.Boot 'Kernel Flags' ''