Dear Curtis, thank you for your input and apologies for this late follow up.
Following your suggestion I tried a few things to force WPF Toolkit to load the WPF toolkit types explicitly, and the solution was to replace the default
where Xxxxxxx is replaced by the real namespace of the target resource (cf. the WPF toolkit source).
I did this for all xmlns calls that I had in both controls and resource dictionaries and it seems to have fixed the issue, so we will distribute this fix in the next update.
I am posting the solution here as it might help other plugin developers, and you might as well be interested to use this trick to avoid ambiguities.