With groups I assume that you are talking about "question groups", right?
There is something called randomization group. These groups can be totally independent of the question groups. Just give all questions that should be randomized among each other the same name in the "randomization group" field and they will be randomized among each other, no matter if they are in the same question group or not.
I answer at the LimeSurvey forum in my spare time, I'm not a LimeSurvey GmbH employee.
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