I apologize for speaking so quickly before. I checked with Shaun so that I could fully understand the problem and it appears that simply upgrading to 4.5.2 when it's available will *not* solve the Repository issue. There are 2 ways to enable AJAX support for a module, letting the core framework do it, or build it into the module itself. When the core framework does it, it cannot know much at all about each individual module, so it does the best it can, it wraps the entire module in an AJAX UpdatePanel. There is a known limitation with streaming content from within an UpdatePanel. You can search on the ASP.NET AJAX forums for more information. Since the Repository module uses a streaming method for both uploading and download, allowing the core to wrap the entire module in an UpdatePanel results in the problem you are seeing.
The 4.5.2 release will include some changes to the core AJAX framework to provide module developers more granular control over which *parts* of their module should be wrapped in an UpdatePanel and which should not. Additionally, there will be changes to the URLControl which uses the same core streaming functions to upload/download content as the Repository Module does. However, this requires code changes in the module itself.
So, the current Repository version 3.01.10 cannot support AJAX by simply checking the 'supports partial rendering' option.
Also, I've already submitted a new release of the Repository module to the Release Process, so the upcoming version of the Repository module, 3.01.12 will also *not* support AJAX by simply checking the 'supports partial rendering' option.
Finally, once 4.5.2 is close to being ready, and as soon as I can understand the code changes I need to make, I will submit a 3.01.13 version of the Repository to the Release Process that *will* include built-in AJAX support.
Sorry for the confusion earlier, I didn't fully understand the issue, but that didn't stop me from replying :) Hopefully this will make this clearer regarding AJAX support in the Repository module.