Did you ever find a solution this this problem? I think I am having the same issue with CF10 Ent on Win2008/IIS7 connecting to Oracle. Almost every day all the sites with a database connection (i.e., CFQUERY) timeout and what looks like loses connection for about 3-9 minutes. I have been tearing my hair out trying to find why.
It also sounds EXACTLY like this Stackoverflow thread where one user said he traced it back to an actual hardware issue.
I am beginning to think it is somethign like that because I have tried EVERYTHING...stress testing, app pool changes in IIS, Max pooled statements changes in CF, running every diagnostic and log you can think of (Jprofiler, Jconsole, Server Monitor, logging all database call, NETSTAT, etc) and have found nothing. In the Failed Request Tracking I see a suspicious error like this during the 500 event (probably when CFQUERY times out): The specified network name is no longer available. (0x80070040). I have seen similar messages in other Failed Request tracking logs such as: An operation was attempted on a nonexistent network connection. (0x800704cd).
What does all this mean? By the way we are on VMware if it matters. Everything was rock solid for years and years until we moved onto either a) VMware, or b) Win2008 / IIS 7 or a combination of the two.
Update: Finally resolved my issue here: http://forums.adobe.com/message/6060877#6060877