Links not working when publishing a flash swf file with ISA server 2006

The right way to do it has probably already passed by and is too late.  What you should have done it use Split-DNS so that the Intranet Site uses the same domain name as it does from the external Internet (intranet.ourcompany.co.uk).  Since it would use the same name no matter where the user is comming from the whole problem would simply never have existed.
As it is now all you can do is try to patch it up by using the Link Translation features in the Publishing Rule Properties.

Maybe that would have been the best way to do it but publishing the intranet was never envisaged years aog when it was first set up. The problem we have is that the link translation works perfectly from the old intranet homepage with is a plain html page, it is only a problem now that this has been replaced with a flash page. I assume that the publishing rule looks at the code for the page and translates any links it finds in accordance with the setting within the rule, but I assume that it treats the swf file that is embedded in the home page simply as an image rather than looking at it as a seperate piece of code. What I need is a way to make it look at  the code within the swf and translate those links as well.

I believe you are correct in how ISA sees the Flash component.
The only option I see is to go with the Split-DNS.  Then have the Flash component edited to use the Public FQDN in the links.  The Split-DNS will make sure that the internal users resolve that FQDN correctly to the private IP of the Site so that they go directly to the correct IP# and not try to make a "u-turn" through the firewall and trhe publishing rule.
The Split-DNS is very simple to do, you guys just have to be willing to do it.

thanks for your comments, I am happy to go with the split DNS. Do you know of a guide for setting it up or is it as simple as adding a record into our internal dns for intranet.oucompany.co.uk pointing to the ip address of the intranet server?

Do forget that after this is done that the link in that Flash thing needs to be adjusted to reflect the Public spelling of the link.
It is also possible (can't say for sure) but you may no longer need the Link translation settings in the Publishing Rule since everyone will access everthing on this site via the Public spelling of everything,...you no longer have to juggle two different namespace spellings.

Thank you for the very quick and easy to follow solution.

Sorry to resurrect this but I have hit a new problem. I have the split dns setup and it sort of works. From an external machines all works fine. From an internal machine, we get a login box when trying to access one of the links - entering the username as domain\username it works ok. Have i messed something in the setup of the split dns for the authentcation?

That is another IE "thing".  Someone who is more intimately and emotionaly involved with IE and its different versions might be able to help better than I, but,...IE will refuse to use Integrated Authentication if it thinks the Site is out on the Internet.  I think it uses some of the same screwed up logic where it arbitrarily decares a Site to be out on the Internet if you use an IP# in the Address bar instead of a "machine name".
I would suggest one of two things:
1. Add the Site's FQDN to the Intranet Zone in IE (not Internet Zone).  Do this from the "Advanced" button.  Use the format *.mysite.com
2. Use can have user on the LAN use the Netbios Name instead of the DNS FQDN.
Either of those two will probably keep IE "happy" and it will use Integrated Authentication like it should.  But if someone more skilled with the details of IE has other suggestions that is fine.