Why is Autocheck.exe taking 3+ minutes at startup

Hi;

I recently set up a new build (specs at the end), and after installing all of the win 7 updates that were available, I started having a recurring problem of sloooooooooow startup.  I seem to have two options now, and neither of them are ideal, which is why I am posting here.

1.  I can reboot and wait the 3-4 minutes, and when windows starts, all seems fine

2.  I can remove autocheck autochk * from the BootExecute registry entry and then it boots fine, but then windows is locked for 3 minutes or so after logon. Nothing responds.  After that it runs fine.

In investigating this situation, I first blamed SMSSinit, but I later discovered that this routine is more of a chaperone for the other processes that are running prior to Winlogon taking over the chaperone duties.  Using MS SDK, I have found that it is Autochck.exe that is the culprit, taking 200-220 seconds on each boot.  I have done the following (and more) to address this issue:

1.  Checked all drives for dirty bits - none found

2.  Ran check disk on all connected drives - no errors found

3.  Disabled Checkdisk in "task manager"

4.  Disabled Checkdisk in registry (when I do this, I get scenario 2 from above)

5.  Restarted the computer in every way I can imagine

6.  Tried a windows repair with my UEFI stick (no love - says it found no issues)

7.  Tried reverting to an earlier restore point (I only had one and it did not solve)

8.  Removed all windows updates I had done (and all Win updates are set to manual only)

9.  Grabbed autochk.exe from another install and put it in the Windows/system32 folder (after taking proper ownership of both) with a new name autochk_safe.exe and pointed registry BootExecute entry to that checkdisk application (thought that was a clever try that I found at another forum)

10.  Ran sfc /scannow - no problems found

11.  Set the BootExecute registry entry to " autocheck autochk /k:C /k:G /k:M /k:R /k:S * ".  I tried this (which should skip autocheck at startup for drives C, G, M, R and S) but it changed nothing.  And that is a disable of all the drives in the system.

If anyone knows what steps I can take here to stop this extended autocheck and not suffer other consequences, it sure would be appreciated.  And yes, I know I can do a full wipe and reinstall, but that should not be necessary as something is causing this and it should be identifiable and resolvable IMO.

Cheers~

C

Build Specs:

Windows 7 Pro 64 bit SP1 (all critical updates installed until I removed them in an attempt to resolve this issue)

ASUS X99 Sabertooth Mobo

i7-5820k CPU

M.2 SM951 Samsung 256GB (Main drive)

Corsair ForceGT 128GB SSD (secondary drive and scratch disk when running on main)

4TB WD Red

4x4TB WD Red in RAID5 configuration (fully initialized and running quite well)

Crucial RAM - 2 x 8GB - 2133Mhz

FireGL Pro V8700 GPU (the elder in this system from 2010)

EVGA Supernova 1000 G2 PSU