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I have been having the same problem that you mention. One solution I found is using Helicon ISAPI_Rewrite module installed in IIS 6.
The idea is to add a header X-If-Modified-Since that is a copy of the header If-Modified-Since. This can be done in ISAPI_Rewrite by adding the following lines to the httpd.ini file:
RewriteCond If-Modified-Since: (.+)
RewriteHeader X-If-Modified-Since: ^$ $1
Then I can access the new header in any ASP script (by the new name) even with 404-redirect turned on.
Something similar may be possible with Microsoft's rewrite module [iis.net] for IIS 7 that some hosting providers now use.
Hope this helps.
[edited by: marcel at 9:32 pm (utc) on Jan. 8, 2010]
[edit reason] Removed specifics [/edit]