While this is a bit late, you really should not be using Singletons. You have found one of the reasons, in complex environments, you can't be sure that they are really singletons.
Additionally, Singletons are simply global wads of data, which totally breaks encapsulation. This makes
unit testing much harder than systems without singletons.
In nearly all cases, the use of Singletons is a mistake and can be avoided simply by deciding not to use them.