Jar Files download Slow in IE but not FireFox

We have an application (PTC Windchill) that uses jar files within the application. These jar files contain our customizations and get downloaded to the users when they require certain functionality within the application. Each time we update our build (update the customizations) new jar files are required to be downloaded to the client. Recently, we have seen an increase in the number of clients that the downloads take an extremely long time. The jar files add up to about 70mb and on a machine that we consider to be working correctly, this takes less than a minute. On some machines, it takes as long as 20 minutes. We are unable to determine what the difference is between computers (both have the same version of JRE, OS, IE and updates etc.). What is interesting, is the files download quickly on FireFox, every time on every machine. We initially thought this was an IE issue, but we can't pin point it. Also, the files transfer fine through the OS so we don't believe it is network or NIC related. This started out as just a few computers but seems to be growing. We have found upgrading to Apache 2.x.x from 1.3.27 fixes the problem, but breaks something else in our application, therefor is not a solution. This would appear to be an IE and Apache compatibility issue, but why it works with some clients and not others, puzzles us. I was hoping someone out there may have some ideas of what the issue is. It is probably something simple, but not simple to find. Any help is much appreaciated.
Thanks,

It's probably an IE problem.
The installed JREs on the client machines have no relationship with downloading via a browser.
It works fine with firefox because this latter is an open source and frequently upgraded. There are lot of firefox plugins and extensions for downloading tasks: https://addons.mozilla.org/en-US/firefox/search?q=download&status=Array
You can allocate more resources for your server and use a multi-thread donwload servlets but it will not resolve the problems of the client side IE browser.

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