The AjaxControlToolkit has always been a point of pain, seems like almost every time they make a new release they break something. If I had a dollar for every headache that thing gave me over the years I would be rich.
Because it is a strong named assembly it poses problems for easily changing a version because everything in the app that uses it must use the same version and be compiled against that version. In some cases you can make things that used an older version use a newer version by assembly mapping, but I don't think you can make it use an older version that way, and also they messed up their versioning in the past such that they ran out of version numbers as discussed in this article, making it I think impossible to use assembly mapping even for newer versions.
For mojoPortal when we updated to the latest version and changed to use Nuget we had to make the same changes in our add on products to use the new version of ajaxcontroltoolkit and release new versions of our add ons at the same time we released mojoportal so that they all use the same version. As such we cannot go backward easily at this point. One would think that since the ajaxcontrol toolkit has not been updated since Jan 2013 that version would be a stable version, but as you find troubles with it, the expectation is not met.
Unfortunately I don't have any good solution to suggest at this time. We can only hope that a new stable version will come out and we can update to that when it does. It seems that Microsoft is no longer going to maintain it though, this blog post from a few months ago says that DevExpress will maintain it going forward. The article says they will update it frequently but as far as I know they have not yet updated it.
We only use a few features of the toolkit in mojoPortal and in our add ons and as far as I know they are all working fine currently, so nothing is broken in our use of it at the current time. But if DevExpress will come out with an update we will update mojoportal and our add on products at that time to use the newer version in order to try to help you with this problem. I suggest contact DevExpress about the issues you are facing to make sure they get resolved in the next update that they put out.