I'm now almost 2 weeks out without the freezing reoccurring. After another week or so when I have caught up on the backlog I will try reverting the partition back to NTFS and see if the problem comes back.
I still think the vast majority of the symptoms in this thread can be explained by what I found on my system. I agree that many different things can set the problem off. One thing that almost all hardware and software has in common is that it periodically
writes/reads to disk in the background; very often when you click the mouse or use the enter key.
If the disk write corrupts the security structure of NTFS in a way that w7 can't diagnose as an error then that 1 initial error can mushroom into many errors after a period of time causing more and more freezes. Once the index is damaged even reads can cause
freezing. If what you are doing requires a read of a disk sector(s) where the index is damaged in a way that w7 does not see as an error then the os will normally retry the read until it times out. This could be for a very long time if a number of sectors
are involved in the read.
I suspect this condition is probably caused by drive-by malware or a virus that attempts to install something that is a variant of a rootkit which alters the index structure in a way that NTFS doesn't know how handle.
To summarize my solution once again.
Check to see if your system partition is formatted as NTFS
If it is use an older version of chkdsk (xp version) to check the integrity of your system partition. The version of chkdsk bundled with w7 misses some structural damage.
The older chkdsk will not permanently fix the problem it will only confirm that something is wrong with the indexing of the partition.
On my system the index problems found by the older chkdsk were most often related to the extra security structures of NTFS so I tried reformatting the partition to Fat32 in the hope that this type of structure would be more stable. It appears to have worked.
* It may also possibly give malware unobstructed access to your hard disk. I am very security conscious but have cleaned up enough machines to know that malware exists that is capable of getting through the best of defenses. I do not have a very flattering
opinion of "governments" as structured today and am vocal about it in a public way. It would not surprise me if what was occurring on my machine was the result of the good(?) guys instead of the bad.
Anyway if the older chkdsk finds errors backup your data and repartition the drive to Fat32 format and see what happens. You can reformat without losing the data by using a program such as partition magic. The backup is only a safety measure in case something
goes wrong with the reformat. The safer but more time consuming way to do this is to backup the system partition, delete the original system partition, use a wipe program to overwrite the area that had been used, create a new system partition in fat32 format,
restore the backup onto the new partition.
The first time I noticed this type of freezing was while using my browser (firefox) quite a few months ago and quite a few versions back. I connect to the internet via satellite which times out fairly regularly but a new kind of timeout started to happen
occasionally that impacted other programs that were open at the same time which also froze. I was surprised because I didn't think an attempt to get data from the internet could cause all open programs to freeze. Initially I didn't think much about how this
could happen but once I started to understand what was going wrong this made sense.
Everything you access on the internet is cached on your local disk in real time so your browser creates a constant stream of tmp files in the background as you browse. If this constant background disk read/write is stalled then it will impact all open programs
not just your browser. The browser timing out on a site would not affect any other programs. The problem is not necessarily a firefox one. The problem is related to disk writes/reads which use generic routines that are also commonly used by other programs
(and hardware) to read write to the disk.
I don't know the os well enough to pinpoint which routines are involved but MS should easily be able to narrow down the possible suspects.
The way my system is structured none of the data files I create are stored on the system partition, they are stored on a different physical drive. There has been no hint of errors in this type of data and I could often use a file manager to normally access
these drives while it would freeze on the system partition. This suggests to me the problem lies in a routine that is only accessed by the os for internal os read / writes.
Anyway good luck with solving your problems and thanks for documenting your thoughts on the issue here. It helped to resolve my issues. This is my last response on this issue.