WebService Timeout IIS6

I hope this is the correct forum for this post.
I have a webservice that processes submitted transactional data. The size of the transactions can vary. I purposely created a very large test transaction to use in testing.
On IIS 5, the large transaction runs fine (after tweaking the httpRuntime executionTimeout setting in web.config).
On IIS 6, the requests fails after approxmiately 2.25 minutes with an entry in the Application Event Log from ASP.NET indicating "HTTPException: request timed out".
I have been working with MS on this for over a week. I have verified that I have correctly set all the time out options on my website and the application pool it is using (they are pushed to 15 minutes). I have verified that these settings are working by putting the webservice to "sleep" for 25 minutes, and the timeout error occurs at the 15 minute mark.
I have traced the source of the error to a call to a particular dll we built, which does some intensive recursive processing. Once this part of the code is reached, the service fails in approxmiately 1 min 45 secs (+ approx. 10% in some cases). I tested to see if I could find the actual source of the error, and I cannot. To check to see if it was taking too long on the call from our service, I tried putting the calling function to sleep for 5 minutes. The result was that the calling function slept for the 5 minutes then invoked the method on the DLL and failed with the same error approx 105 seconds later. I then tried putting the DLL method to sleep for 5 minutes, with the same result: the thread slept for 5 minutes and then failed once it started the actual processing after approx 105 seconds.
The error being thrown from inside the code is "Thread was being aborted. ---> System.Threading.ThreadAbortException: Thread was being aborted."
Checks on the stack trace from the error show that the error is occurring in different places--that is, the code does not consistently perform the same number of recursive calls before failing, and the action the code is performing when the error occurs differs from test to test.
I have tried re-setting the stack space to 1 MB on w3wp.exe, since it appears that the stack space on IIS 5 was 1 MB, but in IIS 6 it is only 256 kb, but that change did not make any difference.
It almost sounds to me like something is pinging this process to see if it is working, and after not receiving a reply, it aborts the thread. Note: I have pinging disabled on the applicationPool being used.

The webservice is built in C#, VS2005. The particular DLL where this issue is occurring is C#, VS2003.
As noted it runs fine in IIS 5 on a Windows 2000 Server.
The failure occurs on IIS 6 on a Windows 2003 Server.

Any pointers or suggestions would be appreciated.