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There shouldn't be any interference problems as long as your dongles use different addresses. Don't make the mistake of assuming that changing the PIN will solve this problem, it won't.
There fact that USB doesn't work well for you is likely a bug in your application, such as implicitly relying on the delay introduced by the BT comms for your controls.
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It seems like the rate of the control loop depends on the execution time of its contents rather than on wall time. This would result in a fragile system whose gain parameters strongly depend on things such as the type of connection. To fix this, instead of making your sleep time constant, check the time and sleep until it's time for the next step.