I had an issue today deploying applications for a client from SCCM. The packages had a number of files using file extensions and directories that are blocked in IIS 7.0 by default. Took awhile but I found how to fix this from a bunch of sites. What you want to look for is in the IIS W3v log files in C:\inetpub\logs\LogFiles\W3SVC1 look for 404 7, 404 8, or 404 11 (search for 404). If you see these you are being “request filtered”
This is a post describing what I was seeing
http://social.technet.microsoft.com/Forums/en-US/configmgrswdist/thread/e3c06b14-d0b8-4b4c-9a52-7f920de06f8e
Following links I fixed some of the errors by editing the applicationhost.config file but it was painful. I found this link which shows you how to run appcmd statements to do this automatically
http://technet.microsoft.com/en-us/library/cc754791(WS.10).aspx
The commands are
appcmd set config /section:requestfiltering /fileExtensions.applyToWebDAV:false
appcmd set config /section:requestfiltering /allowdoubleescaping:true
appcmd set config /section:requestfiltering /hiddensegments.applyToWebDAV:false
Then run iisreset and you should be good. I also had issues getting the packages repushed out to machines once the bit.tmp files showed up so instead of troubleshooting I just reimaged.
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