Curse 3.0 and 4.0 appear to be unable to pass through a Microsoft ISA server 2006 Proxy using integrated windows domain authentication.

Even though the client gets its proxy settings correctly from IE, after a packet capture analysis, it appears it does not forward the currently logged on User Credentials when the proxy sends a NTLM Authentication challenge to the application (yes I'm in a domain, hence the Proxy and NTLM auth on the proxy), the proxy returns an error 407 Proxy Auth required.

Is there any way to fix this? a registry toggle or does it necessitate an application modification?

The v3 client is not being developed.  For the v4 client, there's an ability to report bugs from within the client and on the login page, your best bet is to use that functionality and then follow up on the ticket that's submitted.

Will do, I have to do it from elsewhere tho, the client can't even send a ticket when behind the proxy because of this

This has been fixed in the latest version of v4. Thanks for the report.