To use the approach favored by your manager, this is an excellent question, but it sounds like your manager is not particularly interested in complimenting you in the first place. Her compliments are not compliments at all, but rather are softeners that are designed to make you more receptive to her criticism.
Some managers have been advised to give criticism only when packaging it with some positive feedback. As a result, they use a throwaway compliment, and then hit employees with the zinger. This patently obvious approach is patently ridiculous and tends to generate just the kind of reaction that you are describing.
This is the type of issue that you should discuss with your manager. Let her know that you enjoy the work, and then add that you are interested in having more feedback, not only in terms of constructive criticism, but also in terms of the areas in which you are performing well.
It is possible that your manager needed some feedback to upgrade her skills in this area, and it will not take long for you to see if she has heard you. If you start to receive some bona fide compliments, be sure to give you manager some bona fide thanks for providing them.
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