It seems like when trying to open 2 windows from a succession of windows.open calls, it only allows the first window to open and deletes the reference to the second window. I know this probably sounds a little kludgy, but we do need to have that second popup.
Any ideas?
Unfortunately we are addressing a user-case, where ie6 on the user end has popup blocker enabled.
IE6 makes it sound like it's a corporate installation. Assuming that's true, contact your administrators and have group policy set your internal website to be in the Intranet zone, and turn off the popup blocker for that zone.
EDIT: I just realized that you probably are using a blank ('') window name for both windows:
var win = window.open(url, '', 'blah=1');
var win2 = window.open(url2, '', 'stuff=1'); //later
This is probably handled with different windows in browsers other than IE6.
If that does not work, you might consider injecting divs that display on top of your content (instead of using popups), which is considered a better practice.
The IE pop-up blocker, by default, only allows one new window to be opened per user-initiated-action (i.e. a click on some element). If you try to open two new windows in the same handler in response to a single user-initiated-action, only the first window will successfully be opened. This is by design.
There is an override key that users can use: on IE6 I think it is CTRL, but it might be CTRL+ALT because it got changed in later versions (not sure if that was back-ported or not).
If you go to Tools->Internet Options->Pop-up Blocker->Settings->Blocking Level: and look at the value in the drop-down box for "High" it will tell you the override key in a parenthetical phrase.
In the same settings dialog, you can also add this specific site to the "Allowed sites" list, and then pop-up blocker will let all new window creation attempts on said site succeed. I'm pretty sure this list can also be pre-populated through group policy or IEAK or something like that too. But it's just a list that is stored in the registry, so you can also write log-in scripts that will just add things if they need to be added.
If you have further questions, let me know (I was the developer who implemented the IE pop-up blocker).