A: 

Do the two applications have different domains? IE is preventing the cross-site scripting.

Can you not just have a link to the other site?

EDIT: If this is on Windows Server 2003, then the only way that I've managed to get around it is to disable to enhanced browser security. If this is the case, then you shouldn't really be browsing from a server in the first place.

Edit2:I'm guessing that it is the enhanced browser security that is doing this.
Check out this link: http://support.microsoft.com/kb/815141 on info about it. Your choices are to either to disable it, add an exception for that site, or use another browser.

Jesse
No they both have the same domain one is www.example.com/app1/page.jsp the other is www.example.com/app2/anotherpage.jsp
Omar Kooheji
see edit2 in answer
Jesse
My issue is that there is no "site" to add as an exception. It's complaining about "http://" not another website.
Omar Kooheji
Can you post the code?
Jesse
Unfortunately I can't post the sourceA: Because of an NDAB: The Javaprojects are HugeThe javascript that loads the page is just window.open("URL"); nothing special
Omar Kooheji
Thats irritating I just noticed that SO had parsed "h-t-t-p" as a link...
Omar Kooheji
+1  A: 

IE Enhanced Security Configuration is deliberately designed to prevent general purpose browsing from servers. Folks who want to do workstation-style browsing and just happen to be on a server SKU should disable ESC.

What's the exactly line of code? window.open("http://fullURL", etc), or something like var v=window.open("about:blank"); v.location.href=etc ?

EricLaw -MSFT-
it's window.open("path"); If thats the case then I needn't worry about it though I was just testing that an install had worked by running it locally.
Omar Kooheji
+1  A: 

You need to uninstall "Explorer Enhanced Security", which is on by default in Windows Servers, before IE will act like a normal browser. :)

Workstations shouldn't get this problem.

cdm9002